W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 17 00:41:35 -12 2025 I: pbuilder-time-stamp: 1739796095 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2025.0-2.dsc] I: copying [./gromacs_2025.0.orig-regressiontests.tar.gz] I: copying [./gromacs_2025.0.orig.tar.gz] I: copying [./gromacs_2025.0-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gromacs_2025.0-2.dsc: unsupported subcommand dpkg-source: info: extracting gromacs in gromacs-2025.0 dpkg-source: info: unpacking gromacs_2025.0.orig.tar.gz dpkg-source: info: unpacking gromacs_2025.0.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2025.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2526377/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2526377' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aw8Vny4I/pbuilderrc_axdD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aw8Vny4I/b1 --logfile b1/build.log gromacs_2025.0-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2526377/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.4); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-mpi4py; however: Package python3-mpi4py is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on furo; however: Package furo is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-pygments; however: Package python3-pygments is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-copybutton; however: Package python3-sphinx-copybutton is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-inline-tabs; however: Package python3-sphinx-inline-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} furo{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libabsl20230802{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1t64{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libimath-3-1-29t64{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libjxl0.10{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnghttp3-9{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenexr-3-1-30{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpathplan4{a} libpciaccess0{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsvtav1enc2{a} libsynctex2{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-bs4{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-copybutton{a} python3-sphinx-inline-tabs{a} python3-sphinxcontrib.autoprogram{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-basic-ng{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation fonts-texgyre fonts-texgyre-math javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc publicsuffix python3-gdal python3-lxml python3-matplotlib python3-pil python3-pydot python3-pygraphviz python3-scipy python3-yaml ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 344 newly installed, 0 to remove and 0 not upgraded. Need to get 369 MB of archives. After unpacking 1688 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 11.0.0 [27.6 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 bash-completion all 1:2.16.0-7 [319 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 44 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0049 [42.5 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.5 [2272 B] Get: 46 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.5-2 [2267 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-2 [340 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.5-2 [9907 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 81 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 93 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-1+b1 [23.3 MB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.7-1+b1 [12.0 MB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.7-1+b1 [6851 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2.1 [4519 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.46-4 [276 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 114 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-bs4 all 4.13.3-1 [166 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-4 [616 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 133 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-4 [468 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 furo all 2024.08.06+dfsg-1 [62.8 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-17 [418 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17 [9794 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-17 [14.0 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.0-1 [168 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.42-3 [79.5 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-15.1+b2 [14.9 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-1 [189 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.04.0~dfsg-2+b1 [2351 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.04.0~dfsg-2+b1 [51.0 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.5-1+b1 [11.5 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.5-1+b1 [15.4 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.5-1+b1 [438 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libhwy1t64 arm64 1.2.0-2+b2 [499 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libimath-3-1-29t64 arm64 3.1.12-1+b3 [38.0 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libopenexr-3-1-30 arm64 3.1.5-5.1+b4 [856 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libjxl0.10 arm64 0.10.4-2 [854 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libwmflite-0.2-7 arm64 0.2.13-1.1+b3 [72.0 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libgraphicsmagick-q16-3t64 arm64 1.4+really1.3.45-1+b2 [1079 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 graphicsmagick arm64 1.4+really1.3.45-1+b2 [1080 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b4 [39.4 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b4 [61.4 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.12.0-1 [1672 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3 [491 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-9+b1 [661 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1904.20250204-1 [137 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.83.3-2 [1421 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-3 [415 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b4 [41.4 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b4 [628 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b4 [182 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b4 [198 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b4 [571 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 56.0-1 [58.4 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 56.0-1 [331 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-21 [21.3 MB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 240 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 6.2.4+ds-1 [58.3 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 6.1.2-3 [302 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 247 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 251 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 56.0-1 [67.1 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.5.4-3 [168 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 56.0-1 [28.4 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 56.0-1 [42.2 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 56.0-1 [640 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5+b1 [154 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libmuparser2v5 arm64 2.3.4-1+b1 [127 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libmuparser-dev arm64 2.3.4-1+b1 [33.5 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.6-3 [576 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libopenmpi40 arm64 5.0.6-4 [2088 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 5.0.6-4 [97.1 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.6-3 [3929 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 5.0.6-4 [180 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 5.0.6-4 [1088 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5+b1 [48.2 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.2-1 [1970 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.2-1 [4678 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.1-2 [10.2 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5+b1 [60.6 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5+b1 [106 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 lsb-release all 12.1-1 [5912 B] Get: 311 http://deb.debian.org/debian unstable/main arm64 mpi-default-bin arm64 1.18 [2576 B] Get: 312 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 313 http://deb.debian.org/debian unstable/main arm64 mscgen arm64 0.20-16 [45.1 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.2-1 [505 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.1-2 [26.1 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 322 http://deb.debian.org/debian unstable/main arm64 python3-mpi4py arm64 4.0.3-1 [807 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 324 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.2+ds-2 [135 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.2+ds-2 [4129 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-copybutton all 0.5.2-2 [17.9 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-inline-tabs all 2023.4.21-1 [35.9 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 rdfind arm64 1.6.0-1+b2 [39.1 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 symlinks arm64 1.4-5 [9312 B] Get: 335 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5+b1 [7357 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20250114-1 [22.8 MB] Get: 340 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20250114-1 [1282 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 344 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Fetched 369 MB in 3s (121 MB/s) Preconfiguring packages ... Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20837 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_11.0.0_all.deb ... Unpacking media-types (11.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21847 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_arm64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-7_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-7_arm64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../005-bash-completion_1%3a2.16.0-7_all.deb ... Unpacking bash-completion (1:2.16.0-7) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.4.1-1_arm64.deb ... Unpacking openssl (3.4.1-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../012-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../015-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../017-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../018-libcbor0.10_0.10.2-2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../019-libfido2-1_1.15.0-1+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1+b1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../020-libkrb5support0_1.21.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-4) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../021-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../022-libk5crypto3_1.21.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-4) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../023-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../024-libkrb5-3_1.21.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../025-libgssapi-krb5-2_1.21.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ... Selecting previously unselected package openssh-client. Preparing to unpack .../026-openssh-client_1%3a9.9p1-3_arm64.deb ... Unpacking openssh-client (1:9.9p1-3) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../027-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../028-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../029-ucf_3.0049_all.deb ... Moving old data out of the way Unpacking ucf (3.0049) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../030-architecture-properties_0.2.5_arm64.deb ... Unpacking architecture-properties:arm64 (0.2.5) ... Selecting previously unselected package m4. Preparing to unpack .../031-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../032-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../033-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../034-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../035-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package chrpath. Preparing to unpack .../036-chrpath_0.18-1_arm64.deb ... Unpacking chrpath (0.18-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../037-cmake-data_3.31.5-2_all.deb ... Unpacking cmake-data (3.31.5-2) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../038-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../039-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../040-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../041-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../042-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../043-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../044-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../045-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../046-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../047-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../048-libnghttp3-9_1.6.0-2_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.6.0-2) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../049-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../050-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../051-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../052-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../053-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../054-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../055-libcurl4t64_8.12.1-2_arm64.deb ... Unpacking libcurl4t64:arm64 (8.12.1-2) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../056-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../057-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../058-libuv1t64_1.50.0-2_arm64.deb ... Unpacking libuv1t64:arm64 (1.50.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../059-cmake_3.31.5-2_arm64.deb ... Unpacking cmake (3.31.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../060-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../061-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../062-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../063-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../064-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../065-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../066-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../067-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../068-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../069-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../070-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../071-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../072-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../073-python3-more-itertools_10.6.0-1_all.deb ... Unpacking python3-more-itertools (10.6.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../074-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../075-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../076-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../077-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../078-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../079-python3-pkg-resources_75.6.0-1_all.deb ... Unpacking python3-pkg-resources (75.6.0-1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../080-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../081-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../082-python3-setuptools_75.6.0-1_all.deb ... Unpacking python3-setuptools (75.6.0-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../083-dh-python_6.20250108_all.deb ... Unpacking dh-python (6.20250108) ... Selecting previously unselected package xml-core. Preparing to unpack .../084-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package docutils-common. Preparing to unpack .../085-docutils-common_0.21.2+dfsg-2_all.deb ... Unpacking docutils-common (0.21.2+dfsg-2) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../086-libz3-4_4.13.3-1_arm64.deb ... Unpacking libz3-4:arm64 (4.13.3-1) ... Selecting previously unselected package libllvm19:arm64. Preparing to unpack .../087-libllvm19_1%3a19.1.7-1+b1_arm64.deb ... Unpacking libllvm19:arm64 (1:19.1.7-1+b1) ... Selecting previously unselected package libclang-cpp19. Preparing to unpack .../088-libclang-cpp19_1%3a19.1.7-1+b1_arm64.deb ... Unpacking libclang-cpp19 (1:19.1.7-1+b1) ... Selecting previously unselected package libclang1-19. Preparing to unpack .../089-libclang1-19_1%3a19.1.7-1+b1_arm64.deb ... Unpacking libclang1-19 (1:19.1.7-1+b1) ... Selecting previously unselected package libfmt10:arm64. Preparing to unpack .../090-libfmt10_10.1.1+ds1-4_arm64.deb ... Unpacking libfmt10:arm64 (10.1.1+ds1-4) ... Selecting previously unselected package doxygen. Preparing to unpack .../091-doxygen_1.9.8+ds-2.1_arm64.deb ... Unpacking doxygen (1.9.8+ds-2.1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../092-libpng16-16t64_1.6.46-4_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.46-4) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../093-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../094-libfontenc1_1%3a1.1.8-1+b2_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1+b2) ... Selecting previously unselected package x11-common. Preparing to unpack .../095-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../096-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../097-xfonts-utils_1%3a7.7+7_arm64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../098-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../099-fontconfig-config_2.15.0-2_arm64.deb ... Unpacking fontconfig-config (2.15.0-2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../100-libfontconfig1_2.15.0-2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../101-fontconfig_2.15.0-2_arm64.deb ... Unpacking fontconfig (2.15.0-2) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../102-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package python3-soupsieve. Preparing to unpack .../103-python3-soupsieve_2.6-1_all.deb ... Unpacking python3-soupsieve (2.6-1) ... Selecting previously unselected package python3-bs4. Preparing to unpack .../104-python3-bs4_4.13.3-1_all.deb ... Unpacking python3-bs4 (4.13.3-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../105-python3-pygments_2.18.0+dfsg-2_all.deb ... Unpacking python3-pygments (2.18.0+dfsg-2) ... Selecting previously unselected package python3-defusedxml. Preparing to unpack .../106-python3-defusedxml_0.7.1-3_all.deb ... Unpacking python3-defusedxml (0.7.1-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../107-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../108-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../109-libjs-sphinxdoc_8.1.3-4_all.deb ... Unpacking libjs-sphinxdoc (8.1.3-4) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../110-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../111-sphinx-common_8.1.3-4_all.deb ... Unpacking sphinx-common (8.1.3-4) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../112-python3-alabaster_0.7.16-0.1_all.deb ... Unpacking python3-alabaster (0.7.16-0.1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../113-python-babel-localedata_2.17.0-1_all.deb ... Unpacking python-babel-localedata (2.17.0-1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../114-python3-babel_2.17.0-1_all.deb ... Unpacking python3-babel (2.17.0-1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../115-python3-roman_5.0-1_all.deb ... Unpacking python3-roman (5.0-1) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../116-python3-docutils_0.21.2+dfsg-2_all.deb ... Unpacking python3-docutils (0.21.2+dfsg-2) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../117-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../118-python3-markupsafe_2.1.5-1+b3_arm64.deb ... Unpacking python3-markupsafe (2.1.5-1+b3) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../119-python3-jinja2_3.1.5-2_all.deb ... Unpacking python3-jinja2 (3.1.5-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../120-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../121-python3-certifi_2025.1.31+ds-1_all.deb ... Unpacking python3-certifi (2025.1.31+ds-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../122-python3-charset-normalizer_3.4.0-1+b1_arm64.deb ... Unpacking python3-charset-normalizer (3.4.0-1+b1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../123-python3-idna_3.10-1_all.deb ... Unpacking python3-idna (3.10-1) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../124-python3-urllib3_2.3.0-1_all.deb ... Unpacking python3-urllib3 (2.3.0-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../125-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3-requests. Preparing to unpack .../126-python3-requests_2.32.3+dfsg-1_all.deb ... Unpacking python3-requests (2.32.3+dfsg-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../127-python3-snowballstemmer_2.2.0-4_all.deb ... Unpacking python3-snowballstemmer (2.2.0-4) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../128-python3-sphinx_8.1.3-4_all.deb ... Unpacking python3-sphinx (8.1.3-4) ... Selecting previously unselected package sphinx-basic-ng. Preparing to unpack .../129-sphinx-basic-ng_1.0.0~beta2-1_all.deb ... Unpacking sphinx-basic-ng (1.0.0~beta2-1) ... Selecting previously unselected package furo. Preparing to unpack .../130-furo_2024.08.06+dfsg-1_all.deb ... Unpacking furo (2024.08.06+dfsg-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../131-libgfortran5_14.2.0-17_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-17) ... Selecting previously unselected package libgfortran-14-dev:arm64. Preparing to unpack .../132-libgfortran-14-dev_14.2.0-17_arm64.deb ... Unpacking libgfortran-14-dev:arm64 (14.2.0-17) ... Selecting previously unselected package gfortran-14-aarch64-linux-gnu. Preparing to unpack .../133-gfortran-14-aarch64-linux-gnu_14.2.0-17_arm64.deb ... Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17) ... Selecting previously unselected package gfortran-14. Preparing to unpack .../134-gfortran-14_14.2.0-17_arm64.deb ... Unpacking gfortran-14 (14.2.0-17) ... Selecting previously unselected package libgs-common. Preparing to unpack .../135-libgs-common_10.04.0~dfsg-2_all.deb ... Unpacking libgs-common (10.04.0~dfsg-2) ... Selecting previously unselected package libgs10-common. Preparing to unpack .../136-libgs10-common_10.04.0~dfsg-2_all.deb ... Unpacking libgs10-common (10.04.0~dfsg-2) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../137-libavahi-common-data_0.8-16_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-16) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../138-libavahi-common3_0.8-16_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-16) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../139-libdbus-1-3_1.16.0-1_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.0-1) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../140-libavahi-client3_0.8-16_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-16) ... Selecting previously unselected package libcups2t64:arm64. Preparing to unpack .../141-libcups2t64_2.4.10-2+b1_arm64.deb ... Unpacking libcups2t64:arm64 (2.4.10-2+b1) ... Selecting previously unselected package libidn12:arm64. Preparing to unpack .../142-libidn12_1.42-3_arm64.deb ... Unpacking libidn12:arm64 (1.42-3) ... Selecting previously unselected package libijs-0.35:arm64. Preparing to unpack .../143-libijs-0.35_0.35-15.1+b2_arm64.deb ... Unpacking libijs-0.35:arm64 (0.35-15.1+b2) ... Selecting previously unselected package libjbig2dec0:arm64. Preparing to unpack .../144-libjbig2dec0_0.20-1+b3_arm64.deb ... Unpacking libjbig2dec0:arm64 (0.20-1+b3) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../145-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../146-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../147-libopenjp2-7_2.5.3-1_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.3-1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../148-libpaper2_2.2.5-0.3+b1_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../149-libdeflate0_1.23-1+b1_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-1+b1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../150-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../151-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../152-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../153-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../154-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../155-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../156-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../157-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../158-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../159-libx11-6_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.10-2) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../160-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../161-libsm6_2%3a1.2.4-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.4-1) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../162-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Selecting previously unselected package libgs10:arm64. Preparing to unpack .../163-libgs10_10.04.0~dfsg-2+b1_arm64.deb ... Unpacking libgs10:arm64 (10.04.0~dfsg-2+b1) ... Selecting previously unselected package ghostscript. Preparing to unpack .../164-ghostscript_10.04.0~dfsg-2+b1_arm64.deb ... Unpacking ghostscript (10.04.0~dfsg-2+b1) ... Selecting previously unselected package libdav1d7:arm64. Preparing to unpack .../165-libdav1d7_1.5.1-1_arm64.deb ... Unpacking libdav1d7:arm64 (1.5.1-1) ... Selecting previously unselected package libheif-plugin-dav1d:arm64. Preparing to unpack .../166-libheif-plugin-dav1d_1.19.5-1+b1_arm64.deb ... Unpacking libheif-plugin-dav1d:arm64 (1.19.5-1+b1) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../167-libde265-0_1.0.15-1+b2_arm64.deb ... Unpacking libde265-0:arm64 (1.0.15-1+b2) ... Selecting previously unselected package libheif-plugin-libde265:arm64. Preparing to unpack .../168-libheif-plugin-libde265_1.19.5-1+b1_arm64.deb ... Unpacking libheif-plugin-libde265:arm64 (1.19.5-1+b1) ... Selecting previously unselected package libheif1:arm64. Preparing to unpack .../169-libheif1_1.19.5-1+b1_arm64.deb ... Unpacking libheif1:arm64 (1.19.5-1+b1) ... Selecting previously unselected package libgif7:arm64. Preparing to unpack .../170-libgif7_5.2.2-1+b1_arm64.deb ... Unpacking libgif7:arm64 (5.2.2-1+b1) ... Selecting previously unselected package libhwy1t64:arm64. Preparing to unpack .../171-libhwy1t64_1.2.0-2+b2_arm64.deb ... Unpacking libhwy1t64:arm64 (1.2.0-2+b2) ... Selecting previously unselected package libimath-3-1-29t64:arm64. Preparing to unpack .../172-libimath-3-1-29t64_3.1.12-1+b3_arm64.deb ... Unpacking libimath-3-1-29t64:arm64 (3.1.12-1+b3) ... Selecting previously unselected package libopenexr-3-1-30:arm64. Preparing to unpack .../173-libopenexr-3-1-30_3.1.5-5.1+b4_arm64.deb ... Unpacking libopenexr-3-1-30:arm64 (3.1.5-5.1+b4) ... Selecting previously unselected package libjxl0.10:arm64. Preparing to unpack .../174-libjxl0.10_0.10.4-2_arm64.deb ... Unpacking libjxl0.10:arm64 (0.10.4-2) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../175-libwebpmux3_1.5.0-0.1_arm64.deb ... Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwmflite-0.2-7:arm64. Preparing to unpack .../176-libwmflite-0.2-7_0.2.13-1.1+b3_arm64.deb ... Unpacking libwmflite-0.2-7:arm64 (0.2.13-1.1+b3) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../177-libxext6_2%3a1.3.4-1+b3_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b3) ... Selecting previously unselected package libgraphicsmagick-q16-3t64. Preparing to unpack .../178-libgraphicsmagick-q16-3t64_1.4+really1.3.45-1+b2_arm64.deb ... Unpacking libgraphicsmagick-q16-3t64 (1.4+really1.3.45-1+b2) ... Selecting previously unselected package graphicsmagick. Preparing to unpack .../179-graphicsmagick_1.4+really1.3.45-1+b2_arm64.deb ... Unpacking graphicsmagick (1.4+really1.3.45-1+b2) ... Selecting previously unselected package libann0. Preparing to unpack .../180-libann0_1.1.2+doc-9+b2_arm64.deb ... Unpacking libann0 (1.1.2+doc-9+b2) ... Selecting previously unselected package libcdt5:arm64. Preparing to unpack .../181-libcdt5_2.42.4-2+b4_arm64.deb ... Unpacking libcdt5:arm64 (2.42.4-2+b4) ... Selecting previously unselected package libcgraph6:arm64. Preparing to unpack .../182-libcgraph6_2.42.4-2+b4_arm64.deb ... Unpacking libcgraph6:arm64 (2.42.4-2+b4) ... Selecting previously unselected package libaom3:arm64. Preparing to unpack .../183-libaom3_3.12.0-1_arm64.deb ... Unpacking libaom3:arm64 (3.12.0-1) ... Selecting previously unselected package libabsl20230802:arm64. Preparing to unpack .../184-libabsl20230802_20230802.1-4_arm64.deb ... Unpacking libabsl20230802:arm64 (20230802.1-4) ... Selecting previously unselected package libgav1-1:arm64. Preparing to unpack .../185-libgav1-1_0.19.0-3_arm64.deb ... Unpacking libgav1-1:arm64 (0.19.0-3) ... Selecting previously unselected package librav1e0.7:arm64. Preparing to unpack .../186-librav1e0.7_0.7.1-9+b1_arm64.deb ... Unpacking librav1e0.7:arm64 (0.7.1-9+b1) ... Selecting previously unselected package libsvtav1enc2:arm64. Preparing to unpack .../187-libsvtav1enc2_2.3.0+dfsg-1_arm64.deb ... Unpacking libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Selecting previously unselected package libyuv0:arm64. Preparing to unpack .../188-libyuv0_0.0.1904.20250204-1_arm64.deb ... Unpacking libyuv0:arm64 (0.0.1904.20250204-1) ... Selecting previously unselected package libavif16:arm64. Preparing to unpack .../189-libavif16_1.1.1-1_arm64.deb ... Unpacking libavif16:arm64 (1.1.1-1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../190-libimagequant0_2.18.0-1+b2_arm64.deb ... Unpacking libimagequant0:arm64 (2.18.0-1+b2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../191-libfribidi0_1.0.16-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.16-1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../192-libglib2.0-0t64_2.83.3-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.83.3-2) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../193-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../194-libharfbuzz0b_10.2.0-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... Selecting previously unselected package libraqm0:arm64. Preparing to unpack .../195-libraqm0_0.10.2-1_arm64.deb ... Unpacking libraqm0:arm64 (0.10.2-1) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../196-libxpm4_1%3a3.5.17-1+b3_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.17-1+b3) ... Selecting previously unselected package libgd3:arm64. Preparing to unpack .../197-libgd3_2.3.3-12+b1_arm64.deb ... Unpacking libgd3:arm64 (2.3.3-12+b1) ... Selecting previously unselected package libgts-0.7-5t64:arm64. Preparing to unpack .../198-libgts-0.7-5t64_0.7.6+darcs121130-5.2+b1_arm64.deb ... Unpacking libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../199-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../200-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../201-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../202-libxrender1_1%3a0.9.10-1.1+b4_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b4) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../203-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../204-libltdl7_2.5.4-3_arm64.deb ... Unpacking libltdl7:arm64 (2.5.4-3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../205-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../206-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../207-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../208-libpango-1.0-0_1.56.1-1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.56.1-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../209-libpangoft2-1.0-0_1.56.1-1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../210-libpangocairo-1.0-0_1.56.1-1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ... Selecting previously unselected package libpathplan4:arm64. Preparing to unpack .../211-libpathplan4_2.42.4-2+b4_arm64.deb ... Unpacking libpathplan4:arm64 (2.42.4-2+b4) ... Selecting previously unselected package libgvc6. Preparing to unpack .../212-libgvc6_2.42.4-2+b4_arm64.deb ... Unpacking libgvc6 (2.42.4-2+b4) ... Selecting previously unselected package libgvpr2:arm64. Preparing to unpack .../213-libgvpr2_2.42.4-2+b4_arm64.deb ... Unpacking libgvpr2:arm64 (2.42.4-2+b4) ... Selecting previously unselected package liblab-gamut1:arm64. Preparing to unpack .../214-liblab-gamut1_2.42.4-2+b4_arm64.deb ... Unpacking liblab-gamut1:arm64 (2.42.4-2+b4) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../215-libxmu6_2%3a1.1.3-3+b4_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.3-3+b4) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../216-libxaw7_2%3a1.0.16-1_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.16-1) ... Selecting previously unselected package graphviz. Preparing to unpack .../217-graphviz_2.42.4-2+b4_arm64.deb ... Unpacking graphviz (2.42.4-2+b4) ... Selecting previously unselected package libnl-3-200:arm64. Preparing to unpack .../218-libnl-3-200_3.7.0-0.3+b1_arm64.deb ... Unpacking libnl-3-200:arm64 (3.7.0-0.3+b1) ... Selecting previously unselected package libnl-route-3-200:arm64. Preparing to unpack .../219-libnl-route-3-200_3.7.0-0.3+b1_arm64.deb ... Unpacking libnl-route-3-200:arm64 (3.7.0-0.3+b1) ... Selecting previously unselected package libibverbs1:arm64. Preparing to unpack .../220-libibverbs1_56.0-1_arm64.deb ... Unpacking libibverbs1:arm64 (56.0-1) ... Selecting previously unselected package ibverbs-providers:arm64. Preparing to unpack .../221-ibverbs-providers_56.0-1_arm64.deb ... Unpacking ibverbs-providers:arm64 (56.0-1) ... Selecting previously unselected package libllvm17t64:arm64. Preparing to unpack .../222-libllvm17t64_1%3a17.0.6-21_arm64.deb ... Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... Selecting previously unselected package libamd-comgr2:arm64. Preparing to unpack .../223-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_arm64.deb ... Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../224-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../225-libdrm2_2.4.123-1_arm64.deb ... Unpacking libdrm2:arm64 (2.4.123-1) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../226-libdrm-amdgpu1_2.4.123-1_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.123-1) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../227-libnuma1_2.0.18-1+b1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.18-1+b1) ... Selecting previously unselected package libhsakmt1:arm64. Preparing to unpack .../228-libhsakmt1_6.2.4+ds-1_arm64.deb ... Unpacking libhsakmt1:arm64 (6.2.4+ds-1) ... Selecting previously unselected package libhsa-runtime64-1:arm64. Preparing to unpack .../229-libhsa-runtime64-1_6.1.2-3_arm64.deb ... Unpacking libhsa-runtime64-1:arm64 (6.1.2-3) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../230-libamdhip64-5_5.7.1-5_arm64.deb ... Unpacking libamdhip64-5 (5.7.1-5) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../231-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../232-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../233-libblas-dev_3.12.1-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.1-2) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../234-libboost1.83-dev_1.83.0-4.1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-4.1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../235-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../236-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../237-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../238-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-core-2.1-7t64:arm64. Preparing to unpack .../239-libevent-core-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-extra-2.1-7t64:arm64. Preparing to unpack .../240-libevent-extra-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. Preparing to unpack .../241-libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-openssl-2.1-7t64:arm64. Preparing to unpack .../242-libevent-openssl-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../243-libevent-dev_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-dev (2.1.12-stable-10+b1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../244-libexpat1-dev_2.6.4-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.4-1) ... Selecting previously unselected package librdmacm1t64:arm64. Preparing to unpack .../245-librdmacm1t64_56.0-1_arm64.deb ... Unpacking librdmacm1t64:arm64 (56.0-1) ... Selecting previously unselected package libfabric1:arm64. Preparing to unpack .../246-libfabric1_1.17.0-3.1_arm64.deb ... Unpacking libfabric1:arm64 (1.17.0-3.1) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../247-libfftw3-double3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-long3:arm64. Preparing to unpack .../248-libfftw3-long3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-long3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-single3:arm64. Preparing to unpack .../249-libfftw3-single3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-single3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-bin. Preparing to unpack .../250-libfftw3-bin_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-bin (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-dev:arm64. Preparing to unpack .../251-libfftw3-dev_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-dev:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfontbox-java. Preparing to unpack .../252-libfontbox-java_1%3a1.8.16-5_all.deb ... Unpacking libfontbox-java (1:1.8.16-5) ... Selecting previously unselected package libhwloc15:arm64. Preparing to unpack .../253-libhwloc15_2.11.2-1_arm64.deb ... Unpacking libhwloc15:arm64 (2.11.2-1) ... Selecting previously unselected package libnuma-dev:arm64. Preparing to unpack .../254-libnuma-dev_2.0.18-1+b1_arm64.deb ... Unpacking libnuma-dev:arm64 (2.0.18-1+b1) ... Selecting previously unselected package libltdl-dev:arm64. Preparing to unpack .../255-libltdl-dev_2.5.4-3_arm64.deb ... Unpacking libltdl-dev:arm64 (2.5.4-3) ... Selecting previously unselected package libhwloc-dev:arm64. Preparing to unpack .../256-libhwloc-dev_2.11.2-1_arm64.deb ... Unpacking libhwloc-dev:arm64 (2.11.2-1) ... Selecting previously unselected package libpciaccess0:arm64. Preparing to unpack .../257-libpciaccess0_0.17-3+b3_arm64.deb ... Unpacking libpciaccess0:arm64 (0.17-3+b3) ... Selecting previously unselected package libxnvctrl0:arm64. Preparing to unpack .../258-libxnvctrl0_535.171.04-1+b2_arm64.deb ... Unpacking libxnvctrl0:arm64 (535.171.04-1+b2) ... Selecting previously unselected package ocl-icd-libopencl1:arm64. Preparing to unpack .../259-ocl-icd-libopencl1_2.3.2-1+b2_arm64.deb ... Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1+b2) ... Selecting previously unselected package libhwloc-plugins:arm64. Preparing to unpack .../260-libhwloc-plugins_2.11.2-1_arm64.deb ... Unpacking libhwloc-plugins:arm64 (2.11.2-1) ... Selecting previously unselected package libibumad3:arm64. Preparing to unpack .../261-libibumad3_56.0-1_arm64.deb ... Unpacking libibumad3:arm64 (56.0-1) ... Selecting previously unselected package libibmad5:arm64. Preparing to unpack .../262-libibmad5_56.0-1_arm64.deb ... Unpacking libibmad5:arm64 (56.0-1) ... Selecting previously unselected package libnl-3-dev:arm64. Preparing to unpack .../263-libnl-3-dev_3.7.0-0.3+b1_arm64.deb ... Unpacking libnl-3-dev:arm64 (3.7.0-0.3+b1) ... Selecting previously unselected package libnl-route-3-dev:arm64. Preparing to unpack .../264-libnl-route-3-dev_3.7.0-0.3+b1_arm64.deb ... Unpacking libnl-route-3-dev:arm64 (3.7.0-0.3+b1) ... Selecting previously unselected package libibverbs-dev:arm64. Preparing to unpack .../265-libibverbs-dev_56.0-1_arm64.deb ... Unpacking libibverbs-dev:arm64 (56.0-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../266-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libkpathsea6:arm64. Preparing to unpack .../267-libkpathsea6_2024.20240313.70630+ds-5+b1_arm64.deb ... Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-5+b1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../268-liblapack3_3.12.1-2_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../269-liblapack-dev_3.12.1-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.1-2) ... Selecting previously unselected package libmpfi0:arm64. Preparing to unpack .../270-libmpfi0_1.5.4+ds-4_arm64.deb ... Unpacking libmpfi0:arm64 (1.5.4+ds-4) ... Selecting previously unselected package libmunge2:arm64. Preparing to unpack .../271-libmunge2_0.5.16-1_arm64.deb ... Unpacking libmunge2:arm64 (0.5.16-1) ... Selecting previously unselected package libmuparser2v5:arm64. Preparing to unpack .../272-libmuparser2v5_2.3.4-1+b1_arm64.deb ... Unpacking libmuparser2v5:arm64 (2.3.4-1+b1) ... Selecting previously unselected package libmuparser-dev:arm64. Preparing to unpack .../273-libmuparser-dev_2.3.4-1+b1_arm64.deb ... Unpacking libmuparser-dev:arm64 (2.3.4-1+b1) ... Selecting previously unselected package libpmix2t64:arm64. Preparing to unpack .../274-libpmix2t64_5.0.6-3_arm64.deb ... Unpacking libpmix2t64:arm64 (5.0.6-3) ... Selecting previously unselected package libucx0:arm64. Preparing to unpack .../275-libucx0_1.17.0+ds-3_arm64.deb ... Unpacking libucx0:arm64 (1.17.0+ds-3) ... Selecting previously unselected package libopenmpi40:arm64. Preparing to unpack .../276-libopenmpi40_5.0.6-4_arm64.deb ... Unpacking libopenmpi40:arm64 (5.0.6-4) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../277-openmpi-common_5.0.6-4_all.deb ... Unpacking openmpi-common (5.0.6-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../278-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpmix-dev:arm64. Preparing to unpack .../279-libpmix-dev_5.0.6-3_arm64.deb ... Unpacking libpmix-dev:arm64 (5.0.6-3) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../280-openmpi-bin_5.0.6-4_arm64.deb ... Unpacking openmpi-bin (5.0.6-4) ... Selecting previously unselected package libopenmpi-dev:arm64. Preparing to unpack .../281-libopenmpi-dev_5.0.6-4_arm64.deb ... Unpacking libopenmpi-dev:arm64 (5.0.6-4) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../282-libpaper-utils_2.2.5-0.3+b1_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3+b1) ... Selecting previously unselected package libpdfbox-java. Preparing to unpack .../283-libpdfbox-java_1%3a1.8.16-5_all.deb ... Unpacking libpdfbox-java (1:1.8.16-5) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../284-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package libpotrace0:arm64. Preparing to unpack .../285-libpotrace0_1.16-2+b2_arm64.deb ... Unpacking libpotrace0:arm64 (1.16-2+b2) ... Selecting previously unselected package libptexenc1:arm64. Preparing to unpack .../286-libptexenc1_2024.20240313.70630+ds-5+b1_arm64.deb ... Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ... Selecting previously unselected package libpython3.13:arm64. Preparing to unpack .../287-libpython3.13_3.13.2-1_arm64.deb ... Unpacking libpython3.13:arm64 (3.13.2-1) ... Selecting previously unselected package libpython3.13-dev:arm64. Preparing to unpack .../288-libpython3.13-dev_3.13.2-1_arm64.deb ... Unpacking libpython3.13-dev:arm64 (3.13.2-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../289-libpython3-dev_3.13.1-2_arm64.deb ... Unpacking libpython3-dev:arm64 (3.13.1-2) ... Selecting previously unselected package libsynctex2:arm64. Preparing to unpack .../290-libsynctex2_2024.20240313.70630+ds-5+b1_arm64.deb ... Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-5+b1) ... Selecting previously unselected package libteckit0:arm64. Preparing to unpack .../291-libteckit0_2.5.12+ds1-1+b1_arm64.deb ... Unpacking libteckit0:arm64 (2.5.12+ds1-1+b1) ... Selecting previously unselected package libtexlua53-5:arm64. Preparing to unpack .../292-libtexlua53-5_2024.20240313.70630+ds-5+b1_arm64.deb ... Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-5+b1) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../293-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libzzip-0-13t64:arm64. Preparing to unpack .../294-libzzip-0-13t64_0.13.72+dfsg.1-1.3_arm64.deb ... Unpacking libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Selecting previously unselected package lsb-release. Preparing to unpack .../295-lsb-release_12.1-1_all.deb ... Unpacking lsb-release (12.1-1) ... Selecting previously unselected package mpi-default-bin. Preparing to unpack .../296-mpi-default-bin_1.18_arm64.deb ... Unpacking mpi-default-bin (1.18) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../297-mpi-default-dev_1.18_arm64.deb ... Unpacking mpi-default-dev (1.18) ... Selecting previously unselected package mscgen. Preparing to unpack .../298-mscgen_0.20-16_arm64.deb ... Unpacking mscgen (0.20-16) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../299-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../300-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package tex-common. Preparing to unpack .../301-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package preview-latex-style. Preparing to unpack .../302-preview-latex-style_13.2-1_all.deb ... Unpacking preview-latex-style (13.2-1) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../303-pybind11-dev_2.13.6-2_all.deb ... Unpacking pybind11-dev (2.13.6-2) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../304-python3.13-dev_3.13.2-1_arm64.deb ... Unpacking python3.13-dev (3.13.2-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../305-python3-dev_3.13.1-2_arm64.deb ... Unpacking python3-dev (3.13.1-2) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../306-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-mpi4py. Preparing to unpack .../307-python3-mpi4py_4.0.3-1_arm64.deb ... Unpacking python3-mpi4py (4.0.3-1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../308-python3-networkx_3.2.1-5_all.deb ... Unpacking python3-networkx (3.2.1-5) ... Selecting previously unselected package python3-numpy-dev:arm64. Preparing to unpack .../309-python3-numpy-dev_1%3a2.2.2+ds-2_arm64.deb ... Unpacking python3-numpy-dev:arm64 (1:2.2.2+ds-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../310-python3-numpy_1%3a2.2.2+ds-2_arm64.deb ... Unpacking python3-numpy (1:2.2.2+ds-2) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../311-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pybind11. Preparing to unpack .../312-python3-pybind11_2.13.6-2_all.deb ... Unpacking python3-pybind11 (2.13.6-2) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../313-python3-pytest_8.3.4-1_all.deb ... Unpacking python3-pytest (8.3.4-1) ... Selecting previously unselected package python3-sphinx-argparse. Preparing to unpack .../314-python3-sphinx-argparse_0.5.2-1_all.deb ... Unpacking python3-sphinx-argparse (0.5.2-1) ... Selecting previously unselected package python3-sphinx-copybutton. Preparing to unpack .../315-python3-sphinx-copybutton_0.5.2-2_all.deb ... Unpacking python3-sphinx-copybutton (0.5.2-2) ... Selecting previously unselected package python3-sphinx-inline-tabs. Preparing to unpack .../316-python3-sphinx-inline-tabs_2023.4.21-1_all.deb ... Unpacking python3-sphinx-inline-tabs (2023.4.21-1) ... Selecting previously unselected package python3-sphinxcontrib.autoprogram. Preparing to unpack .../317-python3-sphinxcontrib.autoprogram_0.1.9-1_all.deb ... Unpacking python3-sphinxcontrib.autoprogram (0.1.9-1) ... Selecting previously unselected package rdfind. Preparing to unpack .../318-rdfind_1.6.0-1+b2_arm64.deb ... Unpacking rdfind (1.6.0-1+b2) ... Selecting previously unselected package symlinks. Preparing to unpack .../319-symlinks_1.4-5_arm64.deb ... Unpacking symlinks (1.4-5) ... Selecting previously unselected package t1utils. Preparing to unpack .../320-t1utils_1.41-4+b1_arm64.deb ... Unpacking t1utils (1.41-4+b1) ... Selecting previously unselected package tex-gyre. Preparing to unpack .../321-tex-gyre_20180621-6_all.deb ... Unpacking tex-gyre (20180621-6) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../322-texlive-binaries_2024.20240313.70630+ds-5+b1_arm64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-5+b1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../323-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package texlive-base. Preparing to unpack .../324-texlive-base_2024.20250114-1_all.deb ... Unpacking texlive-base (2024.20250114-1) ... Selecting previously unselected package texlive-fonts-recommended. Preparing to unpack .../325-texlive-fonts-recommended_2024.20250114-1_all.deb ... Unpacking texlive-fonts-recommended (2024.20250114-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../326-texlive-latex-base_2024.20250114-1_all.deb ... Unpacking texlive-latex-base (2024.20250114-1) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../327-texlive-latex-recommended_2024.20250114-1_all.deb ... Unpacking texlive-latex-recommended (2024.20250114-1) ... Selecting previously unselected package texlive-pictures. Preparing to unpack .../328-texlive-pictures_2024.20250114-1_all.deb ... Unpacking texlive-pictures (2024.20250114-1) ... Selecting previously unselected package texlive-latex-extra. Preparing to unpack .../329-texlive-latex-extra_2024.20250114-1_all.deb ... Unpacking texlive-latex-extra (2024.20250114-1) ... Setting up libhwy1t64:arm64 (1.2.0-2+b2) ... Setting up media-types (11.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up symlinks (1.4-5) ... Setting up libtext-charwidth-perl:arm64 (0.04-11+b4) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libaom3:arm64 (3.12.0-1) ... Setting up libpciaccess0:arm64 (0.17-3+b3) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libboost1.83-dev:arm64 (1.83.0-4.1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libfftw3-single3:arm64 (3.3.10-2+b1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libwmflite-0.2-7:arm64 (0.2.13-1.1+b3) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libcbor0.10:arm64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:arm64 (0.2.5) ... Setting up libijs-0.35:arm64 (0.35-15.1+b2) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libgs-common (10.04.0~dfsg-2) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up rdfind (1.6.0-1+b2) ... Setting up liblab-gamut1:arm64 (2.42.4-2+b4) ... Setting up libuv1t64:arm64 (1.50.0-2) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libibumad3:arm64 (56.0-1) ... Setting up libdeflate0:arm64 (1.23-1+b1) ... Setting up libfftw3-long3:arm64 (3.3.10-2+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libibmad5:arm64 (56.0-1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up poppler-data (0.4.12-1) ... Setting up libkrb5support0:arm64 (1.21.3-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Feb 17 12:42:42 UTC 2025. Universal Time is now: Mon Feb 17 12:42:42 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libmunge2:arm64 (0.5.16-1) ... Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up libjbig2dec0:arm64 (0.20-1+b3) ... Setting up libteckit0:arm64 (2.5.12+ds1-1+b1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up bash-completion (1:2.16.0-7) ... Setting up libpathplan4:arm64 (2.42.4-2+b4) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-16) ... Setting up libann0 (1.1.2+doc-9+b2) ... Setting up libdbus-1-3:arm64 (1.16.0-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up t1utils (1.41-4+b1) ... Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libproc2-0:arm64 (2:4.0.4-7) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libpng16-16t64:arm64 (1.6.46-4) ... Setting up libhwloc15:arm64 (2.11.2-1) ... Setting up libimath-3-1-29t64:arm64 (3.1.12-1+b3) ... Setting up python3-numpy-dev:arm64 (1:2.2.2+ds-2) ... Setting up libidn12:arm64 (1.42-3) ... Setting up autopoint (0.23.1-1) ... Setting up libmpfi0:arm64 (1.5.4+ds-4) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-4) ... Setting up libltdl7:arm64 (2.5.4-3) ... Setting up libfftw3-double3:arm64 (3.3.10-2+b1) ... Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:arm64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libgif7:arm64 (5.2.2-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up libnuma1:arm64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:arm64 (1.5.1-1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b2) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up librav1e0.7:arm64 (0.7.1-9+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-0.3+b1) ... Setting up openmpi-common (5.0.6-4) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:arm64 (2.5.3-1) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:arm64 (20230802.1-4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.5-2) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libcdt5:arm64 (2.42.4-2+b4) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libcgraph6:arm64 (2.42.4-2+b4) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libpaper2:arm64 (2.2.5-0.3+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libmuparser2v5:arm64 (2.3.4-1+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up lsb-release (12.1-1) ... Setting up libfido2-1:arm64 (1.15.0-1+b1) ... Setting up libde265-0:arm64 (1.0.15-1+b2) ... Setting up openssl (3.4.1-1) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libyuv0:arm64 (0.0.1904.20250204-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libfmt10:arm64 (10.1.1+ds1-4) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2+b2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-17) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libmuparser-dev:arm64 (2.3.4-1+b1) ... Setting up libllvm19:arm64 (1:19.1.7-1+b1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libclang1-19 (1:19.1.7-1+b1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:arm64 (1:3.5.17-1+b3) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.5.4-3) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.83.3-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libllvm17t64:arm64 (1:17.0.6-21) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libopenexr-3-1-30:arm64 (3.1.5-5.1+b4) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libgav1-1:arm64 (0.19.0-3) ... Setting up ucf (3.0049) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:arm64 (2.42.4-2+b4) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up libhwloc-dev:arm64 (2.11.2-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-17) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up libclang-cpp19 (1:19.1.7-1+b1) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libjxl0.10:arm64 (0.10.4-2) ... Setting up libpython3.13:arm64 (3.13.2-1) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libibverbs1:arm64 (56.0-1) ... Setting up libavif16:arm64 (1.1.1-1) ... Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up ibverbs-providers:arm64 (56.0-1) ... Setting up python3.13 (3.13.2-1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libhwloc-plugins:arm64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up doxygen (1.9.8+ds-2.1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libpython3.13-dev:arm64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-4) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libpmix2t64:arm64 (5.0.6-3) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up librdmacm1t64:arm64 (56.0-1) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up python3-soupsieve (2.6-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpmix-dev:arm64 (5.0.6-3) ... Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libxmu6:arm64 (2:1.1.3-3+b4) ... Setting up libpython3-dev:arm64 (3.13.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:arm64 (8.12.1-2) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libibverbs-dev:arm64 (56.0-1) ... Setting up pybind11-dev (2.13.6-2) ... Setting up python3-bs4 (4.13.3-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... Setting up cmake (3.31.5-2) ... Setting up python3-pybind11 (2.13.6-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up python3-setuptools (75.6.0-1) ... Setting up fontconfig-config (2.15.0-2) ... Setting up python3-networkx (3.2.1-5) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up libgs10:arm64 (10.04.0~dfsg-2+b1) ... Setting up dh-python (6.20250108) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up libpango-1.0-0:arm64 (1.56.1-1) ... Setting up ghostscript (10.04.0~dfsg-2+b1) ... Setting up libcairo2:arm64 (1.18.2-2) ... Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ... Setting up texlive-base (2024.20250114-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ... Setting up libopenmpi40:arm64 (5.0.6-4) ... Setting up texlive-latex-base (2024.20250114-1) ... Setting up texlive-latex-recommended (2024.20250114-1) ... Setting up texlive-pictures (2024.20250114-1) ... Setting up texlive-fonts-recommended (2024.20250114-1) ... Setting up openmpi-bin (5.0.6-4) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.18) ... Setting up texlive-latex-extra (2024.20250114-1) ... Setting up python3-mpi4py (4.0.3-1) ... Setting up libopenmpi-dev:arm64 (5.0.6-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up libheif-plugin-libde265:arm64 (1.19.5-1+b1) ... Setting up libheif1:arm64 (1.19.5-1+b1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b4) ... Setting up libheif-plugin-dav1d:arm64 (1.19.5-1+b1) ... Setting up graphviz (2.42.4-2+b4) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.45-1+b2) ... Setting up mscgen (0.20-16) ... Setting up graphicsmagick (1.4+really1.3.45-1+b2) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up python3-sphinx-copybutton (0.5.2-2) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up sphinx-basic-ng (1.0.0~beta2-1) ... Setting up python3-sphinx-inline-tabs (2023.4.21-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Setting up furo (2024.08.06+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gromacs-2025.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2025.0-2_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2025.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (31.9s) -- Generating done (0.7s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (29.6s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (31.6s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (29.3s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j12 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 6%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 6%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 10%] Built target pulling cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 12%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 12%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 16%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/share/template /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/share/template /build/reproducible-path/gromacs-2025.0/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT share/template/CMakeFiles/template.dir/template.cpp.o -MF CMakeFiles/template.dir/template.cpp.o.d -o CMakeFiles/template.dir/template.cpp.o -c /build/reproducible-path/gromacs-2025.0/share/template/template.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/template.dir/link.d CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target template cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -j12 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build [ 0%] Built target internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/comm.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/taskassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/usergpuids.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 14%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 14%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.10 -o ../../lib/libgromacs_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.10.0.0 ../../lib/libgromacs_d.so.10 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -j12 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 77 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest-all.cc /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build [ 0%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 0%] Built target internal_rpc_xdr [ 0%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 3%] Built target tng_io_obj make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 5%] Built target lmfit_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 5%] Built target linearalgebra /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 5%] Built target energyanalysis /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 7%] Built target colvars_objlib [ 9%] Built target options make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 10%] Built target taskassignment [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 62%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 63%] Built target gmxapi [ 64%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 64%] Built target methane-water-integration [ 64%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 64%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 64%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/interactivetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/loggertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpi_printer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stdiohelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stringtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfilemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_device.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_hardware_environment.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/textblockmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o -MF CMakeFiles/testutils.dir/topologyhelpers.cpp.o.d -o CMakeFiles/testutils.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tprfilegenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o -MF CMakeFiles/testutils.dir/trajectoryreader.cpp.o.d -o CMakeFiles/testutils.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/xvgtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/topologyhelpers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energyreader.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energycomparison.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/interactivetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/refdata_tests.cpp /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/testsystems.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/mpitest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp [ 66%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target awh-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroups.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/mdgpugraph.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 71%] Built target mdlib-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/clfftinitializer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target domdec-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/cpuinfo.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/path.cpp [ 72%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target fft-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/accessor_policy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target listed_forces-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target nbnxm-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target hardware-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/gausstransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target mdspan-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 75%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests/usergpuids.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 77%] Built target ewald-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/gammadistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/multidimarray.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target taskassignment-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbcenums.cpp /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target pbcutil-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 79%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" [ 80%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 80%] Built target compat-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 80%] Built target random-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 80%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 81%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target topology-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target options-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_vector_operations.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 [ 83%] Built target math-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/checkpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target correlations-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp [ 84%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 84%] Built target tool-test-with-leaks cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/helpwriting.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 84%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/exactcontinuation.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 85%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setatoms.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 85%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 87%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 87%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 87%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" [ 88%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/settimestep.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" [ 88%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 92%] Built target fileio-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 92%] Built target mdrun-non-integrator-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/setup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" [ 94%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/analysisdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/pairdist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/select.cpp [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -96485697 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 191.7 1: (ns/day) (hour/ns) 1: Performance: 495.419 0.048 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (186 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -89163813 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 187.0 1: (ns/day) (hour/ns) 1: Performance: 738.819 0.032 1: [ OK ] GmxApiTest.RunnerBasicMD (218 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -67127325 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.008 0.004 195.9 1: (ns/day) (hour/ns) 1: Performance: 877.683 0.027 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 189.6 1: (ns/day) (hour/ns) 1: Performance: 3386.549 0.007 1: [ OK ] GmxApiTest.RunnerReinitialize (238 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 989257610 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 189.5 1: (ns/day) (hour/ns) 1: Performance: 591.138 0.041 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 190.8 1: (ns/day) (hour/ns) 1: Performance: 797.059 0.030 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (237 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1300103157 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.008 0.004 196.1 1: (ns/day) (hour/ns) 1: Performance: 209.157 0.115 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 186.6 1: (ns/day) (hour/ns) 1: Performance: 544.034 0.044 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (249 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 1002004399 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (224 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1355 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1385 ms total) 1: [ PASSED ] 9 tests. 1/90 Test #1: GmxapiExternalInterfaceTests .............. Passed 1.42 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -11668133 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (200 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1108108369 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (173 ms) 2: [----------] 2 tests from GmxApiTest (373 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (384 ms total) 2: [ PASSED ] 2 tests. 2/90 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.40 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (11 ms) 3: [----------] 8 tests from NBlibTest (12 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (17 ms) 3: [----------] 1 test from LinearChainDataFixture (17 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (32 ms total) 3: [ PASSED ] 44 tests. 3/90 Test #3: NbLibListedForcesTests .................... Passed 0.05 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/90 Test #4: NbLibSamplesTestArgon ..................... Passed 0.02 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/90 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.05 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/90 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (7 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (9 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (9 ms total) 7: [ PASSED ] 57 tests. 7/90 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (13 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (19 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (5 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (7 ms) 8: [----------] 4 tests from TprReaderTest (47 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (54 ms total) 8: [ PASSED ] 4 tests. 8/90 Test #8: NbLibTprTests ............................. Passed 0.07 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (3 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (3 ms total) 9: [ PASSED ] 20 tests. 9/90 Test #9: NbLibIntegrationTests ..................... Passed 0.02 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/90 Test #10: NbLibIntegratorTests ...................... Passed 0.01 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (2 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (4 ms total) 11: [ PASSED ] 75 tests. 11/90 Test #11: TestUtilsUnitTests ........................ Passed 0.02 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (6 ms) 12: [----------] 1 test from MpiSelfTest (6 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (6 ms total) 12: [ PASSED ] 1 test. 12/90 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.02 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (3 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (6 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (2 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (2 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (1 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (1 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (1 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (17 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/90 Test #13: UtilityUnitTests .......................... Passed 0.04 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (12 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (19 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (32 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (32 ms total) 14: [ PASSED ] 2 tests. 14/90 Test #14: UtilityMpiUnitTests ....................... Passed 0.04 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (22 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (23 ms total) 15: [ PASSED ] 78 tests. 15/90 Test #15: GmxlibTests ............................... Passed 0.04 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (1 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (1 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (1 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (7 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (10 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (24 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (1 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (26 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (5 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (19 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (27 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (27 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (26 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (18 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (14 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (8 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (5 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (211 ms total) 16: [ PASSED ] 1032 tests. 16/90 Test #16: MdlibUnitTest ............................. Passed 0.28 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (0 ms) 17: [----------] 1 test from BiasTest (0 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (40 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (59 ms) 17: [----------] 2 tests from BiasSharingTest (100 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (4 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (9 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (6 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (4 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (4 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (19 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (17 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (19 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (153 ms total) 17: [ PASSED ] 27 tests. 17/90 Test #17: AwhTest ................................... Passed 0.17 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (1 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (1 ms total) 18: [ PASSED ] 18 tests. 18/90 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.01 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (2 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (2 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -68157469 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -1081665 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -1080164729 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -893403265 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (9 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -1143558503 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (14 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -1085292851 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (4 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (37 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (1 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (42 ms total) 19: [ PASSED ] 21 tests. 19/90 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.05 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -16481 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (5 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (7 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 2125192172 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -538279939 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -1383630081 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (7 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 2146951115 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (18 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -1778524817 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -467795970 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (2 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 1037520858 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (40 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -315097661 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (43 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (91 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (117 ms total) 20: [ PASSED ] 16 tests. 20/90 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.14 sec test 21 Start 21: NNPotAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests 21: Test timeout computed to be: 30 21: [==========] Running 12 tests from 4 test suites. 21: [----------] Global test environment set-up. 21: [----------] 1 test from NNPotTest 21: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 21: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from NNPotTest (0 ms total) 21: 21: [----------] 5 tests from NNPotOptionsTest 21: [ RUN ] NNPotOptionsTest.DefaultParameters 21: [ OK ] NNPotOptionsTest.DefaultParameters (4 ms) 21: [ RUN ] NNPotOptionsTest.OptionSetsActive 21: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 21: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 21: [----------] 5 tests from NNPotOptionsTest (5 ms total) 21: 21: [----------] 5 tests from NNPotTopologyPreprocessorTest 21: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 21: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -1544552743 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -194525253 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -25198754 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (8 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -96862425 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (12 ms) 21: [----------] 5 tests from NNPotTopologyPreprocessorTest (27 ms total) 21: 21: [----------] 1 test from NNPotForceProviderTest 21: [ RUN ] NNPotForceProviderTest.CanConstruct 21: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 21: [----------] 1 test from NNPotForceProviderTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 12 tests from 4 test suites ran. (33 ms total) 21: [ PASSED ] 12 tests. 21/90 Test #21: NNPotAppliedForcesUnitTest ................ Passed 0.05 sec test 22 Start 22: AppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 3 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from ElectricFieldTest 22: [ RUN ] ElectricFieldTest.Static 22: [ OK ] ElectricFieldTest.Static (0 ms) 22: [ RUN ] ElectricFieldTest.Oscillating 22: [ OK ] ElectricFieldTest.Oscillating (0 ms) 22: [ RUN ] ElectricFieldTest.Pulsed 22: [ OK ] ElectricFieldTest.Pulsed (0 ms) 22: [----------] 3 tests from ElectricFieldTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 3 tests from 1 test suite ran. (0 ms total) 22: [ PASSED ] 3 tests. 22/90 Test #22: AppliedForcesUnitTest ..................... Passed 0.01 sec test 23 Start 23: ListedForcesTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ListedForcesTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 132 tests from 9 test suites. 23: [----------] Global test environment set-up. 23: [----------] 24 tests from Bond/ListedForcesTest 23: [ RUN ] Bond/ListedForcesTest.Ifunc/0 23: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/1 23: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/2 23: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/3 23: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/4 23: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/5 23: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/6 23: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/7 23: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/8 23: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/9 23: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/10 23: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/11 23: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/12 23: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/13 23: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/14 23: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/15 23: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/16 23: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/17 23: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/18 23: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/19 23: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/20 23: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/21 23: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/22 23: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/23 23: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 23: [----------] 24 tests from Bond/ListedForcesTest (7 ms total) 23: 23: [----------] 33 tests from Angle/ListedForcesTest 23: [ RUN ] Angle/ListedForcesTest.Ifunc/0 23: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/1 23: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/2 23: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/3 23: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/4 23: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/5 23: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/6 23: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/7 23: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/8 23: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/9 23: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/10 23: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/11 23: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/12 23: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/13 23: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/14 23: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/15 23: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/16 23: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/17 23: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/18 23: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/19 23: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/20 23: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/21 23: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/22 23: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/23 23: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/24 23: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/25 23: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/26 23: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/27 23: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/28 23: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/29 23: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/30 23: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/31 23: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/32 23: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 23: [----------] 33 tests from Angle/ListedForcesTest (10 ms total) 23: 23: [----------] 18 tests from Dihedral/ListedForcesTest 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Dihedral/ListedForcesTest (4 ms total) 23: 23: [----------] 12 tests from Polarize/ListedForcesTest 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 23: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 23: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 23: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 23: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 23: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 23: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 23: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 23: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 23: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 23: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 23: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 23: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from Polarize/ListedForcesTest (3 ms total) 23: 23: [----------] 18 tests from Restraints/ListedForcesTest 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 23: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 23: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 23: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 23: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 23: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 23: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 23: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 23: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 23: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 23: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 23: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 23: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 23: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 23: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 23: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 23: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 23: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 23: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Restraints/ListedForcesTest (4 ms total) 23: 23: [----------] 3 tests from BondZeroLength/ListedForcesTest 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 23: 23: [----------] 3 tests from AngleZero/ListedForcesTest 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 23: 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (4 ms total) 23: 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 132 tests from 9 test suites ran. (39 ms total) 23: [ PASSED ] 132 tests. 23/90 Test #23: ListedForcesTest .......................... Passed 0.06 sec test 24 Start 24: NbnxmTests 24: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbnxmTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests 24: Test timeout computed to be: 30 24: [==========] Running 383 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 18 tests from KernelSetupTest 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 24: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 24: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 24: [----------] 18 tests from KernelSetupTest (0 ms total) 24: 24: [----------] 2 tests from SimdEnergyAccumulatorTest 24: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 24: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 24: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 24: 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 24: 24: [----------] 360 tests from Combinations/NbnxmKernelTest 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (7 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (6 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [----------] 360 tests from Combinations/NbnxmKernelTest (389 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 383 tests from 4 test suites ran. (390 ms total) 24: [ PASSED ] 185 tests. 24: [ SKIPPED ] 198 tests, listed below: 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24/90 Test #24: NbnxmTests ................................ Passed 0.41 sec test 25 Start 25: NbnxmGpuTests 25: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 0 tests from 0 test suites. 25: [==========] 0 tests from 0 test suites ran. (0 ms total) 25: [ PASSED ] 0 tests. 25/90 Test #25: NbnxmGpuTests ............................. Passed 0.02 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 26: [----------] 22 tests from ParseCommonArgsTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (6 ms total) 26: [ PASSED ] 60 tests. 26/90 Test #26: CommandLineUnitTests ...................... Passed 0.02 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/90 Test #27: DomDecTests ............................... Passed 0.01 sec test 28 Start 28: DomDecMpiTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (11 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (19 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (23 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (11 ms) 28: [----------] 4 tests from HaloExchangeTest (67 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (67 ms total) 28: [ PASSED ] 4 tests. 28/90 Test #28: DomDecMpiTests ............................ Passed 0.09 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (17 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (7 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (139 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (6 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (16 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (8 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (6 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (6 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (17 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (14 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (7 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (32 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (237 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/90 Test #29: EwaldUnitTests ............................ Passed 0.27 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (3 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (4 ms) 30: [----------] 2 tests from ManyFFTTest (7 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (7 ms) 30: [----------] 1 test from FFTTest (7 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (3 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (9 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (26 ms total) 30: [ PASSED ] 15 tests. 30/90 Test #30: FFTUnitTests .............................. Passed 0.05 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 67 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 67 tests from 22 test suites ran. (0 ms total) 31: [ PASSED ] 67 tests. 31/90 Test #31: GpuUtilsUnitTests ......................... Passed 0.02 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 22 tests from 10 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (0 ms) 32: [----------] 1 test from CpuInfoTest (0 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (8 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (7 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (7 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (7 ms) 32: [----------] 4 tests from HardwareTopologyTest (30 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 1 test from UuidStringTest 32: [ RUN ] UuidStringTest.Works 32: [ OK ] UuidStringTest.Works (0 ms) 32: [----------] 1 test from UuidStringTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (4 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (2 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (5 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (2 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (7 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (7 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (10 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (10 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 22 tests from 10 test suites ran. (63 ms total) 32: [ PASSED ] 22 tests. 32: 32: YOU HAVE 1 DISABLED TEST 32: 32/90 Test #32: HardwareUnitTests ......................... Passed 0.08 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 328 tests from 41 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 8 tests from ComplexNumberTest 33: [ RUN ] ComplexNumberTest.RealComplexMultiply 33: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.RealComplexExp 33: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAdd 33: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexSubtract 33: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexMultiply 33: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexDivision 33: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexConjugate 33: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAbs2 33: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 33: [----------] 8 tests from ComplexNumberTest (1 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (13 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (13 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (28 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (4 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (5 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 22 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.canAddMatrix 33: [ OK ] MatrixTest.canAddMatrix (0 ms) 33: [ RUN ] MatrixTest.canSubstractMatrix 33: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 33: [ RUN ] MatrixTest.canNegateMatrix 33: [ OK ] MatrixTest.canNegateMatrix (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 33: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixMultiplication 33: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 22 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (12 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (12 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 41 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.UsableInConstexpr 33: [ OK ] RVecTest.UsableInConstexpr (0 ms) 33: [----------] 41 tests from RVecTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 328 tests from 41 test suites ran. (51 ms total) 33: [ PASSED ] 328 tests. 33/90 Test #33: MathUnitTests ............................. Passed 0.07 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (3 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (3 ms total) 34: [ PASSED ] 21 tests. 34/90 Test #34: MdrunUtilityUnitTests ..................... Passed 0.02 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (139 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (125 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (30 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (35 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (51 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (43 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (427 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (55 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (40 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (59 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (47 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (54 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (53 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (35 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (347 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (775 ms total) 35: [ PASSED ] 13 tests. 35/90 Test #35: MdrunUtilityMpiUnitTests .................. Passed 0.79 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/90 Test #36: MDSpanTests ............................... Passed 0.01 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 37: [----------] 2 tests from CheckpointDataTest (3 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (0 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (4 ms total) 37: [ PASSED ] 97 tests. 37/90 Test #37: MdtypesUnitTest ........................... Passed 0.02 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (5 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (7 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (3 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (11 ms total) 38: [ PASSED ] 22 tests. 38/90 Test #38: OnlineHelpUnitTests ....................... Passed 0.02 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 112 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 16 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 39: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 39: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (4 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (4 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (2 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 112 tests from 18 test suites ran. (10 ms total) 39: [ PASSED ] 112 tests. 39/90 Test #39: OptionsUnitTests .......................... Passed 0.02 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (5 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (5 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (8 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (13 ms total) 40: [ PASSED ] 37 tests. 40/90 Test #40: PbcutilUnitTest ........................... Passed 0.03 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (2 ms total) 41: [ PASSED ] 44 tests. 41/90 Test #41: RandomUnitTests ........................... Passed 0.02 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/90 Test #42: RestraintTests ............................ Passed 0.01 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (0 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (9 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (9 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (2 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (8 ms) 43: [----------] 10 tests from SplineTableTest/0 (42 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (0 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (0 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (0 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 43: [----------] 10 tests from SplineTableTest/1 (6 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (49 ms total) 43: [ PASSED ] 20 tests. 43/90 Test #43: TableUnitTests ............................ Passed 0.06 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (0 ms total) 44: [ PASSED ] 3 tests. 44/90 Test #44: TaskAssignmentUnitTests ................... Passed 0.01 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (1 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (1 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (1 ms total) 45: [ PASSED ] 6 tests. 45/90 Test #45: GmxTimingTests ............................ Passed 0.01 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (3 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (1 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 46: [----------] 3 tests from IndexTest (7 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (3 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (19 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (30 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/90 Test #46: TopologyTest .............................. Passed 0.05 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (10 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (1 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 47: [----------] 10 tests from PullTest (12 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (12 ms total) 47: [ PASSED ] 10 tests. 47/90 Test #47: PullTest .................................. Passed 0.02 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 288 tests from 22 test suites. 48: [----------] Global test environment set-up. 48: [----------] 9 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadStore 48: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadU 48: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4StoreU 48: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 48: [----------] 9 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (0 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 16 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 48: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 48: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 48: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 48: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsFloat 48: [ OK ] SimdMathTest.generateTestPointsFloat (1 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (0 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (0 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (0 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (0 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (0 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (0 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (0 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (0 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (0 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (0 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (0 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (0 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (0 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (0 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (0 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (15 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] 32 tests from Simd4FloatingpointTest 48: [ RUN ] Simd4FloatingpointTest.setZero 48: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 48: [ RUN ] Simd4FloatingpointTest.set 48: [ OK ] Simd4FloatingpointTest.set (0 ms) 48: [ RUN ] Simd4FloatingpointTest.add 48: [ OK ] Simd4FloatingpointTest.add (0 ms) 48: [ RUN ] Simd4FloatingpointTest.sub 48: [ OK ] Simd4FloatingpointTest.sub (0 ms) 48: [ RUN ] Simd4FloatingpointTest.mul 48: [ OK ] Simd4FloatingpointTest.mul (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fma 48: [ OK ] Simd4FloatingpointTest.fma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fms 48: [ OK ] Simd4FloatingpointTest.fms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnma 48: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnms 48: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.abs 48: [ OK ] Simd4FloatingpointTest.abs (0 ms) 48: [ RUN ] Simd4FloatingpointTest.neg 48: [ OK ] Simd4FloatingpointTest.neg (0 ms) 48: [ RUN ] Simd4FloatingpointTest.and 48: [ OK ] Simd4FloatingpointTest.and (0 ms) 48: [ RUN ] Simd4FloatingpointTest.or 48: [ OK ] Simd4FloatingpointTest.or (0 ms) 48: [ RUN ] Simd4FloatingpointTest.xor 48: [ OK ] Simd4FloatingpointTest.xor (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andNot 48: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 48: [ RUN ] Simd4FloatingpointTest.max 48: [ OK ] Simd4FloatingpointTest.max (0 ms) 48: [ RUN ] Simd4FloatingpointTest.min 48: [ OK ] Simd4FloatingpointTest.min (0 ms) 48: [ RUN ] Simd4FloatingpointTest.round 48: [ OK ] Simd4FloatingpointTest.round (0 ms) 48: [ RUN ] Simd4FloatingpointTest.trunc 48: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 48: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 48: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.selectByNotMask 48: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpNe 48: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLe 48: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLt 48: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andB 48: [ OK ] Simd4FloatingpointTest.andB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.orB 48: [ OK ] Simd4FloatingpointTest.orB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.anyTrue 48: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 48: [ RUN ] Simd4FloatingpointTest.blend 48: [ OK ] Simd4FloatingpointTest.blend (0 ms) 48: [ RUN ] Simd4FloatingpointTest.reduce 48: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 48: [ RUN ] Simd4FloatingpointTest.dotProduct 48: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 48: [ RUN ] Simd4FloatingpointTest.transpose 48: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 48: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 48: 48: [----------] 2 tests from Simd4MathTest 48: [ RUN ] Simd4MathTest.invsqrt 48: [ OK ] Simd4MathTest.invsqrt (0 ms) 48: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 48: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 48: [----------] 2 tests from Simd4MathTest (0 ms total) 48: 48: [----------] 1 test from Simd4VectorOperationsTest 48: [ RUN ] Simd4VectorOperationsTest.norm2 48: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 48: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 288 tests from 22 test suites ran. (16 ms total) 48: [ PASSED ] 288 tests. 48/90 Test #48: SimdUnitTests ............................. Passed 0.03 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/90 Test #49: CompatibilityHelpersTests ................. Passed 0.02 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (6 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (8 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (445 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (226 ms) 50: [----------] 2 tests from GmxChiTest (743 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (6 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (0 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (0 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (0 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (0 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (0 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (0 ms) 50: [----------] 10 tests from MindistTest (11 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (13 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (776 ms total) 50: [ PASSED ] 31 tests. 50/90 Test #50: GmxAnaTest ................................ Passed 0.79 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 257 tests from 16 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ConvertInteractionsTest 51: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 51: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 51: [----------] 1 test from ConvertInteractionsTest (0 ms total) 51: 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (2 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 51: [----------] 4 tests from GenconfTest (4 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to -16826369 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (164 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to 1772871678 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (149 ms) 51: [----------] 2 tests from GenionTest (313 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 51: [----------] 1 test from GenRestrTest (1 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 51: 51: [----------] 3 tests from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Setting the LD random seed to -1400653251 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 2139094207 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (3 ms) 51: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 51: coefficients that do not sum to zero. This does not affect the simulation 51: and can be ignored, unless you are comparing potential energy values with 51: other force field ports and/or MD software. 51: First such dihedral in molecule A, involving atoms 0 2 1 3 51: 51: 51: NOTE 2 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 3 NOTEs 51: Setting the LD random seed to -671089442 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1367343409 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 51: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 51: Setting the LD random seed to -139502341 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1878878197 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (9 ms) 51: [----------] 3 tests from GromppDirectiveTest (14 ms total) 51: 51: [----------] 6 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (4 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 51: [----------] 6 tests from InsertMoleculesTest (11 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartitioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (0 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (8 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (5 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (4 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (6 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (6 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (5 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (2 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (87 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (5 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (11 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (12 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (12 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (51 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (5 ms) 51: [----------] 6 tests from SolvateTest (98 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) 51: 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (8 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (2 ms) 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest (92 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (16 ms total) 51: 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 51: Setting the LD random seed to -1107824777 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (11 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 51: Setting the LD random seed to -252257677 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -616103977 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1073748132 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (3 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 51: Setting the LD random seed to 737442431 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (9 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 51: Setting the LD random seed to -303621001 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1734588378 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (11 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 51: Setting the LD random seed to 1466821610 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (8 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 51: Setting the LD random seed to -327565353 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1879577153 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (8 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 51: Setting the LD random seed to -1443501213 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -80355378 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (8 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 51: Setting the LD random seed to 2141150639 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -7353553 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (11 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 51: Setting the LD random seed to -1445266697 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -739303507 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 51: Setting the LD random seed to -679746465 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -4718691 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 51: Setting the LD random seed to -1085990 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 2138814397 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (7 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 51: Setting the LD random seed to -171966788 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -805322795 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -1191448577 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1604288187 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -1107338370 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -557316 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 51: Setting the LD random seed to -92293730 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 51: Setting the LD random seed to -564469801 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -674243042 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 51: Setting the LD random seed to -171982901 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (9 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -34398214 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -21526537 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 51: Setting the LD random seed to -12664837 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (8 ms) 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (146 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 257 tests from 16 test suites ran. (789 ms total) 51: [ PASSED ] 217 tests. 51: [ SKIPPED ] 40 tests, listed below: 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51/90 Test #51: GmxPreprocessTests ........................ Passed 0.81 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (29 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (59 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (60 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (56 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (61 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (64 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (879 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (879 ms total) 52: [ PASSED ] 30 tests. 52/90 Test #52: Pdb2gmx1Test .............................. Passed 0.89 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (37 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (516 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (27 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (548 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (1065 ms total) 53: [ PASSED ] 40 tests. 53/90 Test #53: Pdb2gmx2Test .............................. Passed 1.08 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (29 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (32 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (30 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (28 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (32 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (60 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (352 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (28 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (30 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (65 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (337 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (21 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (22 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (25 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (28 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (175 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (17 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (17 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (61 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (174 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (52 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (284 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (47 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (560 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (1497 ms total) 54: [ PASSED ] 39 tests. 54/90 Test #54: Pdb2gmx3Test .............................. Passed 1.51 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (72 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (31 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (11 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (13 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (1 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (46 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (19 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (53 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (11 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (30 ms) 55: [----------] 10 tests from AutocorrTest (292 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (4 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (6 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (1 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (1 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (3 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (6 ms) 55: [----------] 10 tests from ExpfitTest (27 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (333 ms total) 55: [ PASSED ] 21 tests. 55/90 Test #55: CorrelationsTest .......................... Passed 0.35 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (2 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (3 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 56: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (0 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from LifetimeModuleTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (18 ms total) 56: [ PASSED ] 69 tests. 56/90 Test #56: AnalysisDataUnitTests ..................... Passed 0.03 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (2 ms) 57: [----------] 1 test from OutputSelectorDeathTest (2 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (4 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (0 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 57: [----------] 5 tests from SetAtomsTest (5 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (5 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (7 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (38 ms total) 57: [ PASSED ] 67 tests. 57/90 Test #57: CoordinateIOTests ......................... Passed 0.05 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 393 tests from 21 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (5 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 58: [----------] 11 tests from AngleModuleTest (21 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) 58: [----------] 5 tests from ClustsizeTest (6 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (7 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (4 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (14 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (2 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (5 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (4 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (4 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (5 ms) 58: [----------] 6 tests from DistanceModuleTest (25 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (3 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (40 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (40 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (81 ms total) 58: 58: [----------] 13 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (7 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -575507538 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (17 ms) 58: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.100 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 58: Analyzed 21 frames, last time 2.000 58: Setting the LD random seed to -33556993 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (19 ms) 58: [ RUN ] MsdModuleTest.trestartLessThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -262913 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartLessThanDt (11 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -291369 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (14 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 1974271463 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (12 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1035984834 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (14 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2125201115 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (13 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -272662754 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (13 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -281205013 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (14 ms) 58: [----------] 13 tests from MsdModuleTest (144 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 58: [----------] 9 tests from PairDistanceModuleTest (13 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (10 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (9 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (4 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (13 ms) 58: [----------] 5 tests from RdfModuleTest (48 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (6 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (5 ms) 58: [----------] 5 tests from SasaModuleTest (24 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (3 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 58: [----------] 8 tests from SelectModuleTest (15 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (6 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 58: [----------] 10 tests from SurfaceAreaTest (12 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Setting the LD random seed to 1409056702 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (185 ms) 58: [----------] 4 tests from TopologyInformation (187 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 58: [----------] 4 tests from TrajectoryModuleTest (6 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 192 tests from MoleculeTests/DsspModuleTest 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (9 ms) 58: [----------] 192 tests from MoleculeTests/DsspModuleTest (2110 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (11 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (3 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (19 ms total) 58: 58: [----------] 96 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (11 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/6 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/6 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/7 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/7 (11 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/8 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/8 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/9 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/9 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/10 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/10 (13 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/11 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/11 (6 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/12 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/12 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/13 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/13 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/14 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/14 (11 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/15 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/15 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/16 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/16 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/17 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/17 (12 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/18 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/18 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/19 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/19 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/20 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/20 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/21 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/21 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/22 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/22 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/23 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/23 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/24 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/24 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/25 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/25 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/26 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/26 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/27 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/27 (6 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/28 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/28 (12 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/29 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/29 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/30 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/30 (6 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/31 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/31 (11 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/32 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/32 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/33 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/33 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/34 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/34 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/35 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/35 (50 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/36 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/36 (50 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/37 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/37 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/38 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/38 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/39 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/39 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/40 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/40 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/41 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/41 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/42 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/42 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/43 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/43 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/44 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/44 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/45 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/45 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/46 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/46 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/47 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/47 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/48 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/48 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/49 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/49 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/50 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/50 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/51 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/51 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/52 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/52 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/53 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/53 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/54 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/54 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/55 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/55 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/56 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/56 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/57 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/57 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/58 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/58 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/59 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/59 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/60 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/60 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/61 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/61 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/62 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/62 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/63 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/63 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/64 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/64 (41 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/65 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/65 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/66 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/66 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/67 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/67 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/68 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/68 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/69 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/69 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/70 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/70 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/71 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/71 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/72 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/72 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/73 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/73 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/74 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/74 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/75 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/75 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/76 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/76 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/77 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/77 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/78 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/78 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/79 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/79 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/80 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/80 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/81 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/81 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/82 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/82 (41 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/83 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/83 (40 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/84 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/84 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/85 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/85 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/86 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/86 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/87 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/87 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/88 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/88 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/89 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/89 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/90 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/90 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/91 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/91 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/92 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/92 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/93 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/93 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/94 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/94 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/95 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/95 (50 ms) 58: [----------] 96 tests from HBondTests/HbondModuleTest (3634 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (167 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (42 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (224 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 393 tests from 21 test suites ran. (6597 ms total) 58: [ PASSED ] 393 tests. 58/90 Test #58: TrajectoryAnalysisUnitTests ............... Passed 6.62 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 12 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 137 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (7 ms) 59: [----------] 1 test from DhdlTest (8 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 137 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (8 ms) 59: [----------] 1 test from OriresTest (8 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 59: [----------] 5 tests from EnergyTest (5 ms total) 59: 59: [----------] 3 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (118 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (71 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (82 ms) 59: [----------] 3 tests from ViscosityTest (272 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 12 tests from 5 test suites ran. (295 ms total) 59: [ PASSED ] 12 tests. 59/90 Test #59: EnergyAnalysisUnitTests ................... Passed 0.31 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 63 tests from 8 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -138674193 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = -138674193 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com: not available 60: posres-comB: not available 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: nnpot: 60: active = false 60: modelfile = model.pt 60: input-group = System 60: model-input1 = 60: model-input2 = 60: model-input3 = 60: model-input4 = 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 46382 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 60: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 60: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 60: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 60: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 60: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 60: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 60: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 60: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 60: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 60: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 60: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 60: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 60: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 60: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 60: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 60: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 60: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 60: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 60: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 60: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 60: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 60: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 60: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 60: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 60: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 60: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 60: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 60: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 60: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 60: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 60: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 60: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 60: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 60: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 60: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 60: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 60: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 60: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 60: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 60: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 60: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 60: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 60: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 60: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 60: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 60: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 60: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 60: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 60: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 60: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 60: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 60: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 60: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 60: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 60: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 60: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 60: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 60: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 60: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 60: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 60: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 60: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: NN Potential: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (5 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 60: [----------] 2 tests from DumpTest (6 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (1 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (2 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (0 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (0 ms) 60: [----------] 7 tests from GmxMakeNdx (6 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -302141613 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (0 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -25356449 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (211 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -328197 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (203 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -46684193 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (183 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -538609164 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (183 ms) 60: [----------] 4 tests from ConvertTprTest (782 ms total) 60: 60: [----------] 1 test from ConvertTprNoVelocityTest 60: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: 60: NOTE 3 [file lysozyme.top, line 1465]: 60: Zero-step energy minimization will alter the coordinates before 60: calculating the energy. If you just want the energy of a single point, 60: try zero-step MD (with unconstrained_start = yes). To do multiple 60: single-point energy evaluations of different configurations of the same 60: topology, use mdrun -rerun. 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -200857 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (190 ms) 60: [----------] 1 test from ConvertTprNoVelocityTest (190 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (4 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (9 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 63 tests from 8 test suites ran. (1400 ms total) 60: [ PASSED ] 63 tests. 60/90 Test #60: ToolUnitTests ............................. Passed 1.41 sec test 61 Start 61: ToolWithLeaksUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests 61: Test timeout computed to be: 1920 61: [==========] Running 2 tests from 2 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from ConvertTprTest 61: [ RUN ] ConvertTprTest.selectIndexTest 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Setting the LD random seed to -1141129475 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprTest.selectIndexTest (170 ms) 61: [----------] 1 test from ConvertTprTest (170 ms total) 61: 61: [----------] 1 test from ConvertTprNoVelocityTest 61: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: 61: NOTE 3 [file lysozyme.top, line 1465]: 61: Zero-step energy minimization will alter the coordinates before 61: calculating the energy. If you just want the energy of a single point, 61: try zero-step MD (with unconstrained_start = yes). To do multiple 61: single-point energy evaluations of different configurations of the same 61: topology, use mdrun -rerun. 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Setting the LD random seed to 515709943 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (171 ms) 61: [----------] 1 test from ConvertTprNoVelocityTest (171 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 2 tests from 2 test suites ran. (341 ms total) 61: [ PASSED ] 2 tests. 61/90 Test #61: ToolWithLeaksUnitTests .................... Passed 0.35 sec test 62 Start 62: FileIOTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/FileIOTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests 62: Test timeout computed to be: 30 62: [==========] Running 421 tests from 17 test suites. 62: [----------] Global test environment set-up. 62: [----------] 4 tests from Checkpoint 62: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 62: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 62: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 62: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripInt64 62: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripReal 62: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 62: [----------] 4 tests from Checkpoint (0 ms total) 62: 62: [----------] 1 test from StructureIOTest 62: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 62: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 62: [----------] 1 test from StructureIOTest (0 ms total) 62: 62: [----------] 2 tests from FileMD5Test 62: [ RUN ] FileMD5Test.CanComputeMD5 62: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 62: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 62: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 62: [----------] 2 tests from FileMD5Test (0 ms total) 62: 62: [----------] 4 tests from FileTypeTest 62: [ RUN ] FileTypeTest.CorrectValueForEmptyString 62: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForNoExtension 62: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 62: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 62: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 62: [----------] 4 tests from FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from ColorMapTest 62: [ RUN ] ColorMapTest.CanReadFromFile 62: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 62: [ RUN ] ColorMapTest.CanWriteToFile 62: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 62: [ RUN ] ColorMapTest.RoundTrip 62: [ OK ] ColorMapTest.RoundTrip (0 ms) 62: [ RUN ] ColorMapTest.SearchWorks 62: [ OK ] ColorMapTest.SearchWorks (0 ms) 62: [----------] 4 tests from ColorMapTest (0 ms total) 62: 62: [----------] 4 tests from MatioTest 62: [ RUN ] MatioTest.CanWriteToFile 62: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 62: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanConvertToNewRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 62: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 62: [----------] 4 tests from MatioTest (1 ms total) 62: 62: [----------] 3 tests from MrcSerializer 62: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 62: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 62: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 62: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 62: [----------] 3 tests from MrcSerializer (0 ms total) 62: 62: [----------] 4 tests from MrcDensityMap 62: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 62: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 62: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 62: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 62: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 62: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 62: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 62: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 62: [----------] 4 tests from MrcDensityMap (1 ms total) 62: 62: [----------] 8 tests from MrcDensityMapHeaderTest 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 62: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.IsSane 62: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 62: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 62: 62: [----------] 10 tests from ReadTest 62: [ RUN ] ReadTest.get_eint_ReadsInteger 62: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_eint64_ReadsInteger 62: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsInteger 62: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsFloat 62: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 62: [ RUN ] ReadTest.get_ereal_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not a 62: real value 62: 62: 62: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 62: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 62: [----------] 10 tests from ReadTest (0 ms total) 62: 62: [----------] 3 tests from TimeControlTest 62: [ RUN ] TimeControlTest.UnSetHasNoValue 62: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 62: [ RUN ] TimeControlTest.CanSetValue 62: [ OK ] TimeControlTest.CanSetValue (0 ms) 62: [ RUN ] TimeControlTest.CanUnsetValueAgain 62: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 62: [----------] 3 tests from TimeControlTest (0 ms total) 62: 62: [----------] 1 test from FileIOXdrSerializerTest 62: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 62: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 62: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 62: 62: [----------] 1 test from TngTest 62: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 62: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 62: [----------] 1 test from TngTest (0 ms total) 62: 62: [----------] 4 tests from XvgioTest 62: [ RUN ] XvgioTest.readXvgIntWorks 62: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgRealWorks 62: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 62: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgDeprecatedWorks 62: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 62: [----------] 4 tests from XvgioTest (0 ms total) 62: 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 62: 62: [----------] 360 tests from FileTypeMatch/FileTypeTest 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 62: [----------] 360 tests from FileTypeMatch/FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (1 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (1 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 421 tests from 17 test suites ran. (9 ms total) 62: [ PASSED ] 421 tests. 62/90 Test #62: FileIOTests ............................... Passed 0.03 sec test 63 Start 63: SelectionUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/SelectionUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests 63: Test timeout computed to be: 30 63: [==========] Running 201 tests from 11 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from IndexGroupTest 63: [ RUN ] IndexGroupTest.RemovesDuplicates 63: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 63: [----------] 1 test from IndexGroupTest (0 ms total) 63: 63: [----------] 15 tests from IndexBlockTest 63: [ RUN ] IndexBlockTest.CreatesUnknownBlock 63: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesAtomBlock 63: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesSingleBlock 63: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 63: [----------] 15 tests from IndexBlockTest (3 ms total) 63: 63: [----------] 11 tests from IndexMapTest 63: [ RUN ] IndexMapTest.InitializesAtomBlock 63: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 63: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 63: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 63: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 63: [ RUN ] IndexMapTest.InitializesMoleculeBlock 63: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsSingleBlock 63: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocks 63: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 63: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 63: [ RUN ] IndexMapTest.HandlesMultipleRequests 63: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 63: [----------] 11 tests from IndexMapTest (3 ms total) 63: 63: [----------] 3 tests from IndexGroupsAndNamesTest 63: [ RUN ] IndexGroupsAndNamesTest.containsNames 63: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 63: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 63: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 63: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 63: 63: [----------] 15 tests from NeighborhoodSearchTest 63: [ RUN ] NeighborhoodSearchTest.SimpleSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 63: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchBox 63: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 63: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 63: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 63: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 63: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (22 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 63: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 63: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 63: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 63: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 63: [----------] 15 tests from NeighborhoodSearchTest (52 ms total) 63: 63: [----------] 13 tests from PositionCalculationTest 63: [ RUN ] PositionCalculationTest.ComputesAtomPositions 63: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 63: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionMask 63: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 63: [----------] 13 tests from PositionCalculationTest (4 ms total) 63: 63: [----------] 33 tests from SelectionCollectionTest 63: [ RUN ] SelectionCollectionTest.HandlesNoSelections 63: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 63: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 63: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 63: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 63: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 63: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 63: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 63: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 63: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 63: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 63: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 63: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 63: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 63: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 63: [----------] 33 tests from SelectionCollectionTest (6 ms total) 63: 63: [----------] 14 tests from SelectionCollectionInteractiveTest 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 63: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 63: [----------] 14 tests from SelectionCollectionInteractiveTest (5 ms total) 63: 63: [----------] 70 tests from SelectionCollectionDataTest 63: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 63: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 63: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResnr 63: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 63: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 63: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 63: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesChain 63: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMass 63: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCharge 63: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 63: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 63: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 63: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBeta 63: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResname 63: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 63: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 63: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 63: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 63: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 63: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 63: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 63: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 63: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 63: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 63: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 63: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 63: [----------] 70 tests from SelectionCollectionDataTest (45 ms total) 63: 63: [----------] 17 tests from SelectionOptionTest 63: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 63: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 63: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 63: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 63: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptySelections 63: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 63: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelections 63: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 63: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesAdjuster 63: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 63: [----------] 17 tests from SelectionOptionTest (2 ms total) 63: 63: [----------] 9 tests from SelectionFileOptionTest 63: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 63: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 63: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 63: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 201 tests from 11 test suites ran. (125 ms total) 63: [ PASSED ] 201 tests. 63/90 Test #63: SelectionUnitTests ........................ Passed 0.14 sec test 64 Start 64: MdrunOutputTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunOutputTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 12 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from MdrunTest 64: [ RUN ] MdrunTest.WritesHelp 64: [ OK ] MdrunTest.WritesHelp (13 ms) 64: [----------] 1 test from MdrunTest (13 ms total) 64: 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -1074791769 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 196.5 64: (ns/day) (hour/ns) 64: Performance: 47.005 0.511 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (12 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -47190853 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.000 186.4 64: (ns/day) (hour/ns) 64: Performance: 378.078 0.063 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (4 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to 1337685871 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.000 186.3 64: (ns/day) (hour/ns) 64: Performance: 369.784 0.065 64: Reading frame 0 time 0.000 64: # Atoms 3 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (7 ms) 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (25 ms total) 64: 64: [----------] 2 tests from Argon12/OutputFiles 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 190.6 64: (ns/day) (hour/ns) 64: Performance: 2142.070 0.011 64: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (9 ms) 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 195.2 64: (ns/day) (hour/ns) 64: Performance: 1408.136 0.017 64: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (11 ms) 64: [----------] 2 tests from Argon12/OutputFiles (21 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/Trajectories 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -1107364355 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 197.9 64: (ns/day) (hour/ns) 64: Performance: 109.587 0.219 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (14 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to 1608513373 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 272.443 0.088 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (8 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -173210690 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 197.8 64: (ns/day) (hour/ns) 64: Performance: 113.708 0.211 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (11 ms) 64: [----------] 3 tests from MdrunCanWrite/Trajectories (34 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to 2130165325 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 188.8 64: (ns/day) (hour/ns) 64: Performance: 363.478 0.066 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (9 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: The Berendsen barostat does not generate any strictly correct ensemble, 64: and should not be used for new production simulations (in our opinion). 64: We recommend using the C-rescale barostat instead. 64: 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1606697 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 188.5 64: (ns/day) (hour/ns) 64: Performance: 373.211 0.064 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (11 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1099573308 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 189.1 64: (ns/day) (hour/ns) 64: Performance: 356.681 0.067 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (6 ms) 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories (27 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 12 tests from 5 test suites ran. (153 ms total) 64: [ PASSED ] 12 tests. 64/90 Test #64: MdrunOutputTests .......................... Passed 0.17 sec test 65 Start 65: MdrunModulesTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunModulesTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 15 tests from 3 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from DensityFittingTest 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.8565254e+03 65: Maximum force = 4.5099883e+03 on atom 3 65: Norm of force = 1.6816849e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -184550426 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (5 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -9.8207725e+03 65: Maximum force = 7.3954834e+03 on atom 2 65: Norm of force = 2.7825089e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1074038790 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (6 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (7 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Overriding nsteps with value passed on the command line: 4 steps 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 4 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 5 steps. 65: Potential Energy = -1.0954996e+04 65: Maximum force = 7.4724795e+03 on atom 2 65: Norm of force = 2.7758003e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 1608415070 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (4 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (7 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.8565254e+03 65: Maximum force = 4.5099883e+03 on atom 3 65: Norm of force = 1.6816849e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -77960689 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (5 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -2.7138664e+04 65: Maximum force = 6.7827656e+03 on atom 2 65: Norm of force = 1.9608866e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -51904561 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (55 ms) 65: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: Setting the LD random seed to -36194329 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (5 ms) 65: [ RUN ] DensityFittingTest.CheckpointWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (2) 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -326125605 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.003 0.001 194.1 65: (ns/day) (hour/ns) 65: Performance: 182.932 0.131 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.001 189.3 65: (ns/day) (hour/ns) 65: Performance: 763.565 0.031 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (41 ms) 65: [----------] 9 tests from DensityFittingTest (139 ms total) 65: 65: [----------] 4 tests from MimicTest 65: [ RUN ] MimicTest.OneQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 21 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 183.5 65: (ns/day) (hour/ns) 65: Performance: 415.582 0.058 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 461372487 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.OneQuantumMol (12 ms) 65: [ RUN ] MimicTest.AllQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 21 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 183.8 65: (ns/day) (hour/ns) 65: Performance: 465.794 0.052 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -470573155 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.AllQuantumMol (7 ms) 65: [ RUN ] MimicTest.TwoQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 22 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 183.5 65: (ns/day) (hour/ns) 65: Performance: 474.951 0.051 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1071545087 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.TwoQuantumMol (7 ms) 65: [ RUN ] MimicTest.BondCuts 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 66.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: NVE simulation: will use the initial temperature of 300.368 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 19 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 189.1 65: (ns/day) (hour/ns) 65: Performance: 324.720 0.074 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -33597957 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.BondCuts (12 ms) 65: [----------] 4 tests from MimicTest (41 ms total) 65: 65: [----------] 2 tests from WithIntegrator/ImdTest 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 65: Generating 1-4 interactions: fudge = 1 65: 65: NOTE 1 [file glycine_vacuo.top, line 12]: 65: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 65: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 65: the time step of 2.0e-03 ps. 65: Maybe you forgot to change the constraints mdp option. 65: 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 59273. 65: IMD: -imdwait not set, starting simulation. 65: starting mdrun 'Glycine' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -203452255 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.003 0.002 192.5 65: (ns/day) (hour/ns) 65: Performance: 293.590 0.082 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (69 ms) 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 65: apply to steep. 65: 65: Generating 1-4 interactions: fudge = 1 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 33409. 65: IMD: -imdwait not set, starting simulation. 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = 1.1977061e+03 65: Maximum force = 1.7794875e+04 on atom 9 65: Norm of force = 7.8732895e+03 65: Setting the LD random seed to -16779353 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (58 ms) 65: [----------] 2 tests from WithIntegrator/ImdTest (128 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 15 tests from 3 test suites ran. (335 ms total) 65: [ PASSED ] 15 tests. 65/90 Test #65: MdrunModulesTests ......................... Passed 0.35 sec test 66 Start 66: MdrunIOTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunIOTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 76 tests from 13 test suites. 66: [----------] Global test environment set-up. 66: [----------] 9 tests from GromppTest 66: [ RUN ] GromppTest.EmptyMdpFileWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to 1068490719 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group rest: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -135266373 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group Methanol: Single, 3 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 3.0 280.0 66: 6.0- 270.0 66: Simulated annealing for group SOL: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group Methanol is 7.20 66: Number of degrees of freedom in T-Coupling group SOL is 4.80 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -134234513 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 66: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 66: Setting the LD random seed to 1547690877 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (6 ms) 66: [ RUN ] GromppTest.HandlesMaxwarn 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: The Berendsen thermostat does not generate the correct kinetic energy 66: distribution, and should not be used for new production simulations (in 66: our opinion). We would recommend the V-rescale thermostat. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: There was 1 WARNING 66: Setting the LD random seed to -437257251 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 66: [ RUN ] GromppTest.MaxwarnShouldBePositive 66: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 66: [ RUN ] GromppTest.ValidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 66: There were 3 NOTEs 66: Setting the LD random seed to 2088266463 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 66: [ RUN ] GromppTest.InvalidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 Setting the LD random seed to -70254597 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 66: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 66: Setting the LD random seed to 2061368313 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (6 ms) 66: [----------] 9 tests from GromppTest (30 ms total) 66: 66: [----------] 6 tests from MdrunTerminationTest 66: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -68161793 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.005 198.5 66: (ns/day) (hour/ns) 66: Performance: 47.815 0.502 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.3 66: (ns/day) (hour/ns) 66: Performance: 459.106 0.052 66: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (72 ms) 66: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 1, rlist from 1.032 to 1 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 100 steps, 0.1 ps. 66: 66: Step 11: Run time exceeded 0.000 hours, will terminate the run within 200 steps 66: Setting the LD random seed to -1244160142 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.7 66: (ns/day) (hour/ns) 66: Performance: 1055.428 0.023 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 102 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 100 66: Runtime for the run 0.1 ps 66: Run end step 100 66: Run end time 0.1 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 102 66: Runtime for the run 0.102 ps 66: Run end step 102 66: Run end time 0.102 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 187.9 66: (ns/day) (hour/ns) 66: Performance: 493.941 0.049 66: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (36 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1524992110 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 186.9 66: (ns/day) (hour/ns) 66: Performance: 605.662 0.040 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 192.5 66: (ns/day) (hour/ns) 66: Performance: 427.849 0.056 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 6 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 191.1 66: (ns/day) (hour/ns) 66: Performance: 558.953 0.043 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 8 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 8 66: Runtime for the run 0.008 ps 66: Run end step 8 66: Run end time 0.008 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 191.4 66: (ns/day) (hour/ns) 66: Performance: 584.811 0.041 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: NOTE: 25 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 173.2 66: (ns/day) (hour/ns) 66: Performance: 714.769 0.034 66: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (16 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 2147145843 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.006 198.2 66: (ns/day) (hour/ns) 66: Performance: 40.055 0.599 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 187.4 66: (ns/day) (hour/ns) 66: Performance: 838.861 0.029 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (19 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -426145 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 195.0 66: (ns/day) (hour/ns) 66: Performance: 122.249 0.196 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (7 ms) 66: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -536871114 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 185.8 66: (ns/day) (hour/ns) 66: Performance: 570.989 0.042 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 191.6 66: (ns/day) (hour/ns) 66: Performance: 570.989 0.042 66: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (11 ms) 66: [----------] 6 tests from MdrunTerminationTest (163 ms total) 66: 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 2084.098 0.012 66: trr version: GMX_trn_file (single precision) 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (5 ms) 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.5 66: (ns/day) (hour/ns) 66: Performance: 1576.809 0.015 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (9 ms) 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (14 ms total) 66: 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.131 0.065 199.8 66: (ns/day) (hour/ns) 66: Performance: 22.488 1.067 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.656 1.059 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 20 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.035 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.006 1.091 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (152 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.121 0.061 199.9 66: (ns/day) (hour/ns) 66: Performance: 24.230 0.991 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.815 1.052 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.822 1.052 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (144 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.138 0.069 199.9 66: (ns/day) (hour/ns) 66: Performance: 21.266 1.129 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.854 1.209 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.515 1.170 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (161 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 19 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 199.7 66: (ns/day) (hour/ns) 66: Performance: 97.279 0.247 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 194.2 66: (ns/day) (hour/ns) 66: Performance: 1016.674 0.024 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.7 66: (ns/day) (hour/ns) 66: Performance: 1000.457 0.024 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (27 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.7 66: (ns/day) (hour/ns) 66: Performance: 2173.816 0.011 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 192.8 66: (ns/day) (hour/ns) 66: Performance: 1038.361 0.023 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.9 66: (ns/day) (hour/ns) 66: Performance: 1272.032 0.019 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (11 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.9 66: (ns/day) (hour/ns) 66: Performance: 871.125 0.028 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.002 195.6 66: (ns/day) (hour/ns) 66: Performance: 315.211 0.076 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.4 66: (ns/day) (hour/ns) 66: Performance: 1264.634 0.019 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (15 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.006 0.003 196.4 66: (ns/day) (hour/ns) 66: Performance: 482.163 0.050 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.007 0.004 197.1 66: (ns/day) (hour/ns) 66: Performance: 206.895 0.116 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.7 66: (ns/day) (hour/ns) 66: Performance: 1236.819 0.019 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (23 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.3 66: (ns/day) (hour/ns) 66: Performance: 1619.079 0.015 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.7 66: (ns/day) (hour/ns) 66: Performance: 1395.589 0.017 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.4 66: (ns/day) (hour/ns) 66: Performance: 1052.773 0.023 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (15 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 194.7 66: (ns/day) (hour/ns) 66: Performance: 1034.004 0.023 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 187.7 66: (ns/day) (hour/ns) 66: Performance: 1327.428 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.5 66: (ns/day) (hour/ns) 66: Performance: 1223.365 0.020 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (12 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.008 0.004 196.6 66: (ns/day) (hour/ns) 66: Performance: 368.368 0.065 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.9 66: (ns/day) (hour/ns) 66: Performance: 1330.135 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.5 66: (ns/day) (hour/ns) 66: Performance: 869.963 0.028 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (15 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 195.2 66: (ns/day) (hour/ns) 66: Performance: 1230.151 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.5 66: (ns/day) (hour/ns) 66: Performance: 970.393 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.0 66: (ns/day) (hour/ns) 66: Performance: 850.011 0.028 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (16 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.3 66: (ns/day) (hour/ns) 66: Performance: 1544.396 0.016 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.9 66: (ns/day) (hour/ns) 66: Performance: 971.549 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.4 66: (ns/day) (hour/ns) 66: Performance: 909.253 0.026 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (13 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 198.2 66: (ns/day) (hour/ns) 66: Performance: 218.724 0.110 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.7 66: (ns/day) (hour/ns) 66: Performance: 1344.945 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.6 66: (ns/day) (hour/ns) 66: Performance: 916.407 0.026 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (18 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.5 66: (ns/day) (hour/ns) 66: Performance: 2059.022 0.012 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 1251.051 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.080 0.040 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.446 1.234 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (58 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.167 0.084 199.9 66: (ns/day) (hour/ns) 66: Performance: 17.587 1.365 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.717 1.436 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.046 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.758 1.432 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (195 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.154 0.077 199.9 66: (ns/day) (hour/ns) 66: Performance: 19.014 1.262 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.086 0.043 199.8 66: (ns/day) (hour/ns) 66: Performance: 18.064 1.329 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.083 0.042 199.8 66: (ns/day) (hour/ns) 66: Performance: 18.695 1.284 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (180 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 191.626 0.125 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.1 66: (ns/day) (hour/ns) 66: Performance: 793.164 0.030 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.4 66: (ns/day) (hour/ns) 66: Performance: 742.767 0.032 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (41 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 190.778 0.126 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.5 66: (ns/day) (hour/ns) 66: Performance: 753.928 0.032 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 193.4 66: (ns/day) (hour/ns) 66: Performance: 558.761 0.043 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (38 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 194.8 66: (ns/day) (hour/ns) 66: Performance: 750.103 0.032 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.2 66: (ns/day) (hour/ns) 66: Performance: 741.754 0.032 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 99.269 0.242 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (35 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.003 195.2 66: (ns/day) (hour/ns) 66: Performance: 574.897 0.042 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 193.9 66: (ns/day) (hour/ns) 66: Performance: 345.937 0.069 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.0 66: (ns/day) (hour/ns) 66: Performance: 99.862 0.240 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (48 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.232 0.116 199.9 66: (ns/day) (hour/ns) 66: Performance: 12.659 1.896 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 22 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 193.2 66: (ns/day) (hour/ns) 66: Performance: 541.866 0.044 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.5 66: (ns/day) (hour/ns) 66: Performance: 707.942 0.034 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (182 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.006 0.003 196.0 66: (ns/day) (hour/ns) 66: Performance: 472.656 0.051 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 198.1 66: (ns/day) (hour/ns) 66: Performance: 114.805 0.209 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 98.890 0.243 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (141 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.4 66: (ns/day) (hour/ns) 66: Performance: 188.104 0.128 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.006 198.4 66: (ns/day) (hour/ns) 66: Performance: 139.900 0.172 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.0 66: (ns/day) (hour/ns) 66: Performance: 604.876 0.040 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (57 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.5 66: (ns/day) (hour/ns) 66: Performance: 188.070 0.128 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.008 0.004 197.1 66: (ns/day) (hour/ns) 66: Performance: 190.999 0.126 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.2 66: (ns/day) (hour/ns) 66: Performance: 608.828 0.039 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (80 ms) 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1689 ms total) 66: 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 192.0 66: (ns/day) (hour/ns) 66: Performance: 1021.657 0.023 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.4 66: (ns/day) (hour/ns) 66: Performance: 619.231 0.039 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 192.2 66: (ns/day) (hour/ns) 66: Performance: 497.103 0.048 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (38 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.5 66: (ns/day) (hour/ns) 66: Performance: 122.181 0.196 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.110 0.055 199.7 66: (ns/day) (hour/ns) 66: Performance: 14.103 1.702 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.099 0.050 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.663 1.532 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (149 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.229 0.114 199.9 66: (ns/day) (hour/ns) 66: Performance: 12.829 1.871 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.129 0.065 199.9 66: (ns/day) (hour/ns) 66: Performance: 12.021 1.997 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.123 0.061 199.7 66: (ns/day) (hour/ns) 66: Performance: 12.653 1.897 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (275 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.229 0.115 199.9 66: (ns/day) (hour/ns) 66: Performance: 12.802 1.875 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.130 0.065 199.9 66: (ns/day) (hour/ns) 66: Performance: 11.983 2.003 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.123 0.062 199.7 66: (ns/day) (hour/ns) 66: Performance: 12.641 1.899 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (276 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.070 0.035 199.6 66: (ns/day) (hour/ns) 66: Performance: 41.802 0.574 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 193.2 66: (ns/day) (hour/ns) 66: Performance: 498.775 0.048 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.9 66: (ns/day) (hour/ns) 66: Performance: 625.406 0.038 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (82 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 193.5 66: (ns/day) (hour/ns) 66: Performance: 914.170 0.026 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 76 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.6 66: (ns/day) (hour/ns) 66: Performance: 95.432 0.251 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.008 0.004 196.6 66: (ns/day) (hour/ns) 66: Performance: 192.112 0.125 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (155 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.006 197.4 66: (ns/day) (hour/ns) 66: Performance: 253.888 0.095 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 193.3 66: (ns/day) (hour/ns) 66: Performance: 528.433 0.045 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.2 66: (ns/day) (hour/ns) 66: Performance: 675.537 0.036 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (49 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 194.3 66: (ns/day) (hour/ns) 66: Performance: 796.766 0.030 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.5 66: (ns/day) (hour/ns) 66: Performance: 713.518 0.034 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.3 66: (ns/day) (hour/ns) 66: Performance: 626.848 0.038 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (59 ms) 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1087 ms total) 66: 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.1 66: (ns/day) (hour/ns) 66: Performance: 1674.529 0.014 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.5 66: (ns/day) (hour/ns) 66: Performance: 1346.611 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.009 0.004 197.1 66: (ns/day) (hour/ns) 66: Performance: 175.945 0.136 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (15 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.005 197.6 66: (ns/day) (hour/ns) 66: Performance: 272.400 0.088 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.9 66: (ns/day) (hour/ns) 66: Performance: 1348.838 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.4 66: (ns/day) (hour/ns) 66: Performance: 989.830 0.024 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (16 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 186.6 66: (ns/day) (hour/ns) 66: Performance: 2075.672 0.012 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.006 198.0 66: (ns/day) (hour/ns) 66: Performance: 121.412 0.198 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.5 66: (ns/day) (hour/ns) 66: Performance: 1138.391 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (20 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.6 66: (ns/day) (hour/ns) 66: Performance: 1625.486 0.015 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 1389.051 0.017 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 1068.640 0.022 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (15 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.8 66: (ns/day) (hour/ns) 66: Performance: 1259.320 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.0 66: (ns/day) (hour/ns) 66: Performance: 951.982 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.5 66: (ns/day) (hour/ns) 66: Performance: 857.159 0.028 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (16 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.8 66: (ns/day) (hour/ns) 66: Performance: 1484.838 0.016 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.8 66: (ns/day) (hour/ns) 66: Performance: 963.513 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 187.9 66: (ns/day) (hour/ns) 66: Performance: 867.879 0.028 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (20 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 196.9 66: (ns/day) (hour/ns) 66: Performance: 664.215 0.036 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.5 66: (ns/day) (hour/ns) 66: Performance: 831.589 0.029 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.1 66: (ns/day) (hour/ns) 66: Performance: 692.461 0.035 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (18 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.9 66: (ns/day) (hour/ns) 66: Performance: 947.492 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.4 66: (ns/day) (hour/ns) 66: Performance: 914.351 0.026 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.2 66: (ns/day) (hour/ns) 66: Performance: 796.262 0.030 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (17 ms) 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (140 ms total) 66: 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.002 195.0 66: (ns/day) (hour/ns) 66: Performance: 605.642 0.040 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 197.9 66: (ns/day) (hour/ns) 66: Performance: 117.888 0.204 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.077 0.039 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.142 1.192 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (59 ms) 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.146 0.073 199.9 66: (ns/day) (hour/ns) 66: Performance: 20.145 1.191 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.086 0.043 199.8 66: (ns/day) (hour/ns) 66: Performance: 18.016 1.332 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.351 1.179 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (169 ms) 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (229 ms total) 66: 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.121 0.061 199.8 66: (ns/day) (hour/ns) 66: Performance: 24.156 0.994 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.729 1.056 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.658 1.059 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (148 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.128 0.064 199.8 66: (ns/day) (hour/ns) 66: Performance: 22.948 1.046 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 16 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.035 199.7 66: (ns/day) (hour/ns) 66: Performance: 21.995 1.091 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 16 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.035 199.7 66: (ns/day) (hour/ns) 66: Performance: 21.961 1.093 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (152 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.3 66: (ns/day) (hour/ns) 66: Performance: 73.895 0.325 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.3 66: (ns/day) (hour/ns) 66: Performance: 1173.620 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.8 66: (ns/day) (hour/ns) 66: Performance: 1154.510 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (34 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.0 66: (ns/day) (hour/ns) 66: Performance: 1975.816 0.012 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.2 66: (ns/day) (hour/ns) 66: Performance: 1271.536 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 1095.195 0.022 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (15 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.3 66: (ns/day) (hour/ns) 66: Performance: 1426.063 0.017 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.7 66: (ns/day) (hour/ns) 66: Performance: 881.484 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.4 66: (ns/day) (hour/ns) 66: Performance: 830.318 0.029 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (13 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.003 197.1 66: (ns/day) (hour/ns) 66: Performance: 526.817 0.046 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.4 66: (ns/day) (hour/ns) 66: Performance: 799.581 0.030 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 190.7 66: (ns/day) (hour/ns) 66: Performance: 464.600 0.052 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (21 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.006 198.5 66: (ns/day) (hour/ns) 66: Performance: 266.162 0.090 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.0 66: (ns/day) (hour/ns) 66: Performance: 774.149 0.031 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.8 66: (ns/day) (hour/ns) 66: Performance: 732.261 0.033 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (18 ms) 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (405 ms total) 66: 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 66: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.7 66: (ns/day) (hour/ns) 66: Performance: 182.013 0.132 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.5 66: (ns/day) (hour/ns) 66: Performance: 672.889 0.036 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 662.635 0.036 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (23 ms) 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (23 ms total) 66: 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.5 66: (ns/day) (hour/ns) 66: Performance: 1193.220 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 187.4 66: (ns/day) (hour/ns) 66: Performance: 1000.764 0.024 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.2 66: (ns/day) (hour/ns) 66: Performance: 1028.213 0.023 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (21 ms) 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.3 66: (ns/day) (hour/ns) 66: Performance: 1296.148 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 22 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.013 199.2 66: (ns/day) (hour/ns) 66: Performance: 57.951 0.414 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.046 199.7 66: (ns/day) (hour/ns) 66: Performance: 16.743 1.433 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (74 ms) 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (96 ms total) 66: 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: Setting the AWH bias MC random seed to -75540099 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to -91227140 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.175 0.088 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.758 1.432 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 21 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.014 198.5 66: (ns/day) (hour/ns) 66: Performance: 56.698 0.423 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.0 66: (ns/day) (hour/ns) 66: Performance: 607.015 0.040 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (147 ms) 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: Setting the AWH bias MC random seed to -1645217285 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to 1535114492 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 192.1 66: (ns/day) (hour/ns) 66: Performance: 668.685 0.036 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 188.7 66: (ns/day) (hour/ns) 66: Performance: 586.388 0.041 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.006 197.3 66: (ns/day) (hour/ns) 66: Performance: 134.433 0.179 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (47 ms) 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (194 ms total) 66: 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 66: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 198.7 66: (ns/day) (hour/ns) 66: Performance: 223.704 0.107 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.002 196.7 66: (ns/day) (hour/ns) 66: Performance: 322.473 0.074 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.006 0.003 192.8 66: (ns/day) (hour/ns) 66: Performance: 272.381 0.088 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (55 ms) 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (55 ms total) 66: 66: [----------] 3 tests from Checking/InitialConstraintsTest 66: [ RUN ] Checking/InitialConstraintsTest.Works/0 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -2954755 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 182.7 66: (ns/day) (hour/ns) 66: Performance: 327.508 0.073 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (11 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/1 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -73667133 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.1 66: (ns/day) (hour/ns) 66: Performance: 242.562 0.099 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (8 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: Integrator method md-vv-avek is implemented primarily for validation 66: purposes; for molecular dynamics, you should probably be using md or 66: md-vv 66: 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1099696514 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 198.0 66: (ns/day) (hour/ns) 66: Performance: 26.394 0.909 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (11 ms) 66: [----------] 3 tests from Checking/InitialConstraintsTest (31 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 76 tests from 13 test suites ran. (4266 ms total) 66: [ PASSED ] 76 tests. 66/90 Test #66: MdrunIOTests .............................. Passed 4.28 sec test 67 Start 67: MdrunTestsOneRank 67: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 29 tests from 8 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Generating 1-4 interactions: fudge = 0.5 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -545285163 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 32 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.350 0.175 199.9 67: (ns/day) (hour/ns) 67: Performance: 7.412 3.238 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 21 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.258 0.129 199.9 67: (ns/day) (hour/ns) 67: Performance: 10.054 2.387 67: [ OK ] CompelTest.SwapCanRun (556 ms) 67: [----------] 1 test from CompelTest (556 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 50 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.012 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 14.922 1.608 67: Setting the LD random seed to -100720649 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalBondWorks (18 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 51 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.186 1.580 67: Setting the LD random seed to -20514 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (12 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 50 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.166 1.583 67: Setting the LD random seed to -124010947 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (11 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 48 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.012 0.006 199.1 67: (ns/day) (hour/ns) 67: Performance: 14.515 1.653 67: Setting the LD random seed to -1746010379 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 50 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.168 1.582 67: Setting the LD random seed to 2147483619 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (11 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 51 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.150 1.584 67: Setting the LD random seed to 1793580539 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (12 ms) 67: [----------] 6 tests from BondedInteractionsTest (79 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 41 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.014 0.007 198.9 67: (ns/day) (hour/ns) 67: Performance: 24.213 0.991 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2097119071 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to -38416823 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (14 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: Setting the LD random seed to -1925849603 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.23 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.383 0.192 199.9 67: (ns/day) (hour/ns) 67: Performance: 18.938 1.267 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1549 ms) 67: [----------] 2 tests from BoxDeformationTest (1564 ms total) 67: 67: [----------] 1 test from PositionRestraintCommTest 67: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using 67: verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any of the VCM groups 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any center of mass motion removal group. 67: This may lead to artifacts. 67: In most cases one should use one group for the whole system. 67: 67: Number of degrees of freedom in T-Coupling group System is 29527.73 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Channel_coco in octane membrane' 67: 10 steps, 0.0 ps. 67: Setting the LD random seed to -33622404 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.208 0.104 199.9 67: (ns/day) (hour/ns) 67: Performance: 18.300 1.311 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (346 ms) 67: [----------] 1 test from PositionRestraintCommTest (347 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1413615681 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.013 0.006 197.9 67: (ns/day) (hour/ns) 67: Performance: 66.738 0.360 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -203456833 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.009 0.005 197.0 67: (ns/day) (hour/ns) 67: Performance: 90.670 0.265 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (24041 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1482765 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 198.3 67: (ns/day) (hour/ns) 67: Performance: 75.322 0.319 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -306266113 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.003 0.001 192.7 67: (ns/day) (hour/ns) 67: Performance: 321.437 0.075 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (29 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24071 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 1071398075 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 186.5 67: (ns/day) (hour/ns) 67: Performance: 718.169 0.033 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 2142748511 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 129.8 67: (ns/day) (hour/ns) 67: Performance: 429.777 0.056 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (18 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (18 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 189.7 67: (ns/day) (hour/ns) 67: Performance: 927.350 0.026 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (17 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 189.4 67: (ns/day) (hour/ns) 67: Performance: 964.367 0.025 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (10 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 188.8 67: (ns/day) (hour/ns) 67: Performance: 920.805 0.026 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (17 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.4 67: (ns/day) (hour/ns) 67: Performance: 928.935 0.026 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (10 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.005 197.6 67: (ns/day) (hour/ns) 67: Performance: 144.122 0.167 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (17 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 67: Parrinello-Rahman is not implemented in md-vv. 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.3 67: (ns/day) (hour/ns) 67: Performance: 926.297 0.026 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (12 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.3 67: (ns/day) (hour/ns) 67: Performance: 896.753 0.027 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (13 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.5 67: (ns/day) (hour/ns) 67: Performance: 822.363 0.029 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (21 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.5 67: (ns/day) (hour/ns) 67: Performance: 874.394 0.027 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (36 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 189.4 67: (ns/day) (hour/ns) 67: Performance: 888.932 0.027 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (37 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 189.4 67: (ns/day) (hour/ns) 67: Performance: 888.206 0.027 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (38 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (233 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -268469509 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.020 0.010 198.7 67: (ns/day) (hour/ns) 67: Performance: 153.569 0.156 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (14 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -542412033 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.015 0.007 198.0 67: (ns/day) (hour/ns) 67: Performance: 211.524 0.113 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (11 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -1076512013 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 188.4 67: (ns/day) (hour/ns) 67: Performance: 2529.268 0.009 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (5 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -8748178 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.012 0.006 197.7 67: (ns/day) (hour/ns) 67: Performance: 247.984 0.097 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (10 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (42 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 29 tests from 8 test suites ran. (26973 ms total) 67: [ PASSED ] 28 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/90 Test #67: MdrunTestsOneRank ......................... Passed 26.99 sec test 68 Start 68: MdrunTestsTwoRanks 68: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 29 tests from 8 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from CompelTest 68: [ RUN ] CompelTest.SwapCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Split0 group 'Ch0' contains 83 atoms. 68: Split1 group 'Ch1' contains 83 atoms. 68: Solvent group 'SOL' contains 11931 atoms. 68: Swap group 'NA+' contains 19 atoms. 68: Swap group 'CL-' contains 19 atoms. 68: Number of degrees of freedom in T-Coupling group System is 27869.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Determining initial numbers of ions per compartment. 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -270958611 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 53.9%. 68: The balanceable part of the MD step is 14%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 7.6%. 68: 68: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 8 % of the run time was spent in domain decomposition, 68: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 7 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.549 0.387 399.9 68: (ns/day) (hour/ns) 68: Performance: 3.346 7.173 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 68: 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Copying channel fluxes from checkpoint file data 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.271 0.068 399.4 68: (ns/day) (hour/ns) 68: Performance: 19.101 1.256 68: [ OK ] CompelTest.SwapCanRun (895 ms) 68: [----------] 1 test from CompelTest (895 ms total) 68: 68: [----------] 6 tests from BondedInteractionsTest 68: [ RUN ] BondedInteractionsTest.NormalBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 56 % of the run time was spent in domain decomposition, 68: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.091 0.023 399.6 68: (ns/day) (hour/ns) 68: Performance: 3.808 6.302 68: Setting the LD random seed to 1006331383 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalBondWorks (115 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 79 % of the run time was spent in domain decomposition, 68: 6 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.159 0.040 399.8 68: (ns/day) (hour/ns) 68: Performance: 2.173 11.044 68: Setting the LD random seed to -1612054563 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedBondWorks (87 ms) 68: [ RUN ] BondedInteractionsTest.NormalAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 69 % of the run time was spent in domain decomposition, 68: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.016 399.5 68: (ns/day) (hour/ns) 68: Performance: 5.295 4.532 68: Setting the LD random seed to -38212251 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalAngleWorks (79 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 66 % of the run time was spent in domain decomposition, 68: 8 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.126 0.031 399.7 68: (ns/day) (hour/ns) 68: Performance: 2.745 8.742 68: Setting the LD random seed to 2137849819 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (64 ms) 68: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 91 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.348 0.087 399.9 68: (ns/day) (hour/ns) 68: Performance: 0.993 24.172 68: Setting the LD random seed to -1538265283 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalDihedralWorks (171 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 58 % of the run time was spent in domain decomposition, 68: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.796 0.199 399.9 68: (ns/day) (hour/ns) 68: Performance: 0.434 55.310 68: Setting the LD random seed to -9469954 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (247 ms) 68: [----------] 6 tests from BondedInteractionsTest (767 ms total) 68: 68: [----------] 2 tests from BoxDeformationTest 68: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 0 steps, 0.0 ps. 68: 68: NOTE: 49 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 15 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.401 0.108 370.8 68: (ns/day) (hour/ns) 68: Performance: 1.599 15.013 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2071983479 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Setting gen_seed to -168853796 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (273 ms) 68: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 1293.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 20 steps, 0.0 ps. 68: Setting the LD random seed to -1095540801 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 68: 68: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 68: 68: Estimate for the relative computational load of the PME mesh part: 0.23 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 6.0%. 68: The balanceable part of the MD step is 15%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.9%. 68: 68: 68: Core t (s) Wall t (s) (%) 68: Time: 3.253 0.813 400.0 68: (ns/day) (hour/ns) 68: Performance: 4.462 5.379 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2543 ms) 68: [----------] 2 tests from BoxDeformationTest (2816 ms total) 68: 68: [----------] 1 test from PositionRestraintCommTest 68: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using 68: verlet-buffer-tolerance. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any of the VCM groups 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any center of mass motion removal group. 68: This may lead to artifacts. 68: In most cases one should use one group for the whole system. 68: 68: Number of degrees of freedom in T-Coupling group System is 29527.73 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Channel_coco in octane membrane' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to -663765105 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.453 0.113 399.7 68: (ns/day) (hour/ns) 68: Performance: 16.758 1.432 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (400 ms) 68: [----------] 1 test from PositionRestraintCommTest (400 ms total) 68: 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -647004169 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.95 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.307 0.077 399.7 68: (ns/day) (hour/ns) 68: Performance: 5.633 4.261 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -249660577 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.95 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 6 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.249 0.062 399.4 68: (ns/day) (hour/ns) 68: Performance: 6.923 3.467 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 68: 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (24996 ms) 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -136324121 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.95 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 48 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.119 0.030 398.7 68: (ns/day) (hour/ns) 68: Performance: 14.440 1.662 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2130509067 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.95 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 31 % of the run time was spent in domain decomposition, 68: 8 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.269 0.067 399.6 68: (ns/day) (hour/ns) 68: Performance: 6.419 3.739 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (343 ms) 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (25340 ms total) 68: 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -546964547 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 24 % of the run time was spent in domain decomposition, 68: 7 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.154 0.039 399.4 68: (ns/day) (hour/ns) 68: Performance: 11.214 2.140 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -2102531 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.111 0.028 398.7 68: (ns/day) (hour/ns) 68: Performance: 15.533 1.545 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (163 ms) 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (163 ms total) 68: 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 26.9%. 68: The balanceable part of the MD step is 39%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 10.5%. 68: 68: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 48 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.008 396.5 68: (ns/day) (hour/ns) 68: Performance: 98.088 0.245 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (49 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 44.6%. 68: The balanceable part of the MD step is 44%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 19.6%. 68: 68: NOTE: 19.6 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 12 % of the run time was spent in domain decomposition, 68: 1 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.975 0.500 395.1 68: (ns/day) (hour/ns) 68: Performance: 1.555 15.430 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (963 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 37.9%. 68: The balanceable part of the MD step is 49%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 18.4%. 68: 68: NOTE: 18.4 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 17 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 2.042 0.511 399.8 68: (ns/day) (hour/ns) 68: Performance: 1.522 15.766 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (584 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 13.9%. 68: The balanceable part of the MD step is 4%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.6%. 68: 68: 68: NOTE: 64 % of the run time was spent in domain decomposition, 68: 1 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 14 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.025 0.006 394.7 68: (ns/day) (hour/ns) 68: Performance: 120.872 0.199 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (495 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 13.6%. 68: The balanceable part of the MD step is 44%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.9%. 68: 68: NOTE: 5.9 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 47 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.010 396.9 68: (ns/day) (hour/ns) 68: Performance: 77.839 0.308 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (40 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 68: Parrinello-Rahman is not implemented in md-vv. 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.211 0.053 399.7 68: (ns/day) (hour/ns) 68: Performance: 14.733 1.629 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (204 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in domain decomposition, 68: 1 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 5 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.752 0.188 399.8 68: (ns/day) (hour/ns) 68: Performance: 4.132 5.808 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (337 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.558 0.139 399.9 68: (ns/day) (hour/ns) 68: Performance: 5.575 4.305 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (314 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 2.259 0.567 398.7 68: (ns/day) (hour/ns) 68: Performance: 1.372 17.493 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (706 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 6 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.803 0.451 399.5 68: (ns/day) (hour/ns) 68: Performance: 1.723 13.931 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (516 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 33 % of the run time was spent in domain decomposition, 68: 6 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.323 0.081 398.6 68: (ns/day) (hour/ns) 68: Performance: 9.588 2.503 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (173 ms) 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest (4386 ms total) 68: 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -4198957 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 2.8%. 68: The balanceable part of the MD step is 1%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.0%. 68: 68: 68: NOTE: 75 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.014 398.7 68: (ns/day) (hour/ns) 68: Performance: 110.128 0.218 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (310 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -384827713 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.3%. 68: The balanceable part of the MD step is 1%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.0%. 68: 68: 68: NOTE: 94 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.013 398.5 68: (ns/day) (hour/ns) 68: Performance: 121.263 0.198 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (148 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -1200136198 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 1.1%. 68: The balanceable part of the MD step is 42%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.5%. 68: 68: 68: NOTE: 47 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.008 396.2 68: (ns/day) (hour/ns) 68: Performance: 196.989 0.122 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (19 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 2138537855 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 5.8%. 68: The balanceable part of the MD step is 31%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 1.8%. 68: 68: 68: NOTE: 45 % of the run time was spent in domain decomposition, 68: 4 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.507 0.127 399.8 68: (ns/day) (hour/ns) 68: Performance: 12.266 1.957 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (182 ms) 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (662 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 29 tests from 8 test suites ran. (35497 ms total) 68: [ PASSED ] 28 tests. 68: [ SKIPPED ] 1 test, listed below: 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68/90 Test #68: MdrunTestsTwoRanks ........................ Passed 35.51 sec test 69 Start 69: MdrunSingleRankAlgorithmsTests 69: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 5 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from DispersionCorrectionTest 69: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 30.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 200 steps, 0.4 ps. 69: Setting the LD random seed to 1872608725 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 3 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 12 Constraints with virtual sites to connections, 0 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.016 0.008 198.8 69: (ns/day) (hour/ns) 69: Performance: 4331.200 0.006 69: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (36 ms) 69: [----------] 1 test from DispersionCorrectionTest (36 ms total) 69: 69: [----------] 1 test from OriresTest 69: [ RUN ] OriresTest.OriresCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 518.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 69: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 69: 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to -12861459 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.015 0.008 198.2 69: (ns/day) (hour/ns) 69: Performance: 247.856 0.097 69: [ OK ] OriresTest.OriresCanRun (310 ms) 69: [----------] 1 test from OriresTest (310 ms total) 69: 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 69: Number of degrees of freedom in T-Coupling group rest is 10.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -643179018 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: Searching the wall atom type(s) 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.7 69: (ns/day) (hour/ns) 69: Performance: 407.369 0.059 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 69: 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (40905 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 69: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 69: The supported numbers are > 1. 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 all molecules should be neutral. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 you can only use domain decomposition when there 69: are only small molecules with all bonds constrained (mdrun will check for 69: this). 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -554193128 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.007 0.003 196.7 69: (ns/day) (hour/ns) 69: Performance: 1307.136 0.018 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (16819 ms) 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (57724 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 5 tests from 3 test suites ran. (58098 ms total) 69: [ PASSED ] 5 tests. 69/90 Test #69: MdrunSingleRankAlgorithmsTests ............ Passed 58.11 sec test 70 Start 70: Minimize1RankTests 70: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Minimize1RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.7990997e+01 70: Maximum force = 1.8629692e+02 on atom 13 70: Norm of force = 8.7721836e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (160 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.5862350e+01 70: Maximum force = 4.2726685e+02 on atom 13 70: Norm of force = 1.8452681e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (151 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1937723e+02 70: Maximum force = 9.9988691e+03 on atom 9 70: Norm of force = 4.6167015e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (56 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5174414e+02 70: Maximum force = 7.4208760e+03 on atom 9 70: Norm of force = 3.5692977e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (55 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.5698444e+02 70: Maximum force = 4.5702216e+02 on atom 17 70: Norm of force = 1.8327095e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (12 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06799e+03 on atom 28 70: F-Norm = 4.26914e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.6941235e+02 70: Maximum force = 2.1838167e+02 on atom 17 70: Norm of force = 7.9235206e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (11 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (448 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.7425687e-01 70: Maximum force = 4.0132279e+00 on atom 1 70: Norm of force = 1.6383933e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (7 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 1 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 1 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1939673e+02 70: Maximum force = 9.9704229e+03 on atom 9 70: Norm of force = 4.6227534e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (51 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5625757e+02 70: Maximum force = 7.5018237e+03 on atom 9 70: Norm of force = 3.6139019e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (55 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization has stopped, but the forces have not converged to the 70: requested precision Fmax < 10 (which may not be possible for your system). It 70: stopped because the algorithm tried to make a new step whose size was too 70: small, or there was no change in the energy since last step. Either way, we 70: regard the minimization as converged to within the available machine 70: precision, given your starting configuration and EM parameters. 70: 70: Double precision normally gives you higher accuracy, but this is often not 70: needed for preparing to run molecular dynamics. 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 70: but did not reach the requested Fmax < 10. 70: Potential Energy = 5.6111578e+02 70: Maximum force = 1.2685402e+04 on atom 10 70: Norm of force = 6.0643536e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (56 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (184 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (648 ms total) 70: [ PASSED ] 12 tests. 70/90 Test #70: Minimize1RankTests ........................ Passed 0.67 sec test 71 Start 71: Minimize2RankTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Minimize2RankTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 12 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -4.7990952e+01 71: Maximum force = 1.8629709e+02 on atom 13 71: Norm of force = 8.7721970e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (270 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 3.02331e+02 on atom 3 71: F-Norm = 1.18024e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -5.5862202e+01 71: Maximum force = 4.2727243e+02 on atom 13 71: Norm of force = 1.8452909e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (168 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.1937720e+02 71: Maximum force = 9.9988691e+03 on atom 9 71: Norm of force = 4.6167015e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (397 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: 71: NOTE 3 [file glycine_vacuo.top, line 12]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41575e+04 on atom 10 71: F-Norm = 1.18451e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.5174358e+02 71: Maximum force = 7.4208833e+03 on atom 9 71: Norm of force = 3.5692986e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (107 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.5698444e+02 71: Maximum force = 4.5702219e+02 on atom 17 71: Norm of force = 1.8327095e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (144 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: 71: NOTE 4 [file unknown]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 6 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 1.06799e+03 on atom 28 71: F-Norm = 4.26914e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.6941229e+02 71: Maximum force = 2.1838167e+02 on atom 17 71: Norm of force = 7.9235200e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (461 ms) 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1551 ms total) 71: 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents converged to Fmax < 10 in 1 steps 71: Potential Energy = -9.7425687e-01 71: Maximum force = 4.0132279e+00 on atom 3 71: Norm of force = 1.6383933e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (53 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 4.01323e+00 on atom 3 71: F-Norm = 1.63839e+00 71: 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 71: Potential Energy = -9.9064195e-01 71: Maximum force = 2.5781672e+00 on atom 3 71: Norm of force = 1.0525324e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (128 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: 71: There was 1 WARNING 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.1939664e+02 71: Maximum force = 9.9704229e+03 on atom 9 71: Norm of force = 4.6227537e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (592 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41672e+04 on atom 10 71: F-Norm = 1.19357e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.5625764e+02 71: Maximum force = 7.5018237e+03 on atom 9 71: Norm of force = 3.6139019e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (453 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (47 ms) 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1279 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 2 test suites ran. (2851 ms total) 71: [ PASSED ] 12 tests. 71/90 Test #71: Minimize2RankTests ........................ Passed 2.87 sec test 72 Start 72: MdrunNonIntegratorTests 72: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 46 tests from 3 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from NonbondedBenchTest 72: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 72: SIMD width: 4 72: System size: 3000 atoms 72: Cut-off radius: 1 nm 72: Number of threads: 1 72: Number of iterations: 1 72: Compute energies: no 72: Ewald excl. corr.: analytical 72: 72: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 72: total useful 72: Ewald all geom. 4xM 0.116 0.1163 10.2350 5.4148 72: [ OK ] NonbondedBenchTest.BasicEndToEndTest (15 ms) 72: [----------] 1 test from NonbondedBenchTest (15 ms total) 72: 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.123 0.062 199.8 72: (ns/day) (hour/ns) 72: Performance: 23.771 1.010 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 72: 72: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 62 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.046 0.023 199.8 72: (ns/day) (hour/ns) 72: Performance: 64.024 0.375 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (97 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.138 0.069 199.9 72: (ns/day) (hour/ns) 72: Performance: 21.311 1.126 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 63 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.045 0.023 199.8 72: (ns/day) (hour/ns) 72: Performance: 64.677 0.371 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (99 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.112 0.056 199.9 72: (ns/day) (hour/ns) 72: Performance: 26.123 0.919 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 57 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.050 0.025 199.8 72: (ns/day) (hour/ns) 72: Performance: 58.449 0.411 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (90 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.104 0.052 199.9 72: (ns/day) (hour/ns) 72: Performance: 28.098 0.854 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 25 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 190.9 72: (ns/day) (hour/ns) 72: Performance: 5087.195 0.005 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (61 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.2 72: (ns/day) (hour/ns) 72: Performance: 1923.983 0.012 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 188.0 72: (ns/day) (hour/ns) 72: Performance: 4438.468 0.005 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (166 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.016 0.008 199.1 72: (ns/day) (hour/ns) 72: Performance: 182.997 0.131 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 25 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 187.7 72: (ns/day) (hour/ns) 72: Performance: 4506.652 0.005 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (168 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.014 0.007 198.0 72: (ns/day) (hour/ns) 72: Performance: 213.494 0.112 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 27 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 190.4 72: (ns/day) (hour/ns) 72: Performance: 4145.756 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (176 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.016 0.008 198.5 72: (ns/day) (hour/ns) 72: Performance: 182.061 0.132 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 185.8 72: (ns/day) (hour/ns) 72: Performance: 4516.564 0.005 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (185 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.015 0.008 198.1 72: (ns/day) (hour/ns) 72: Performance: 191.412 0.125 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 22 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 191.8 72: (ns/day) (hour/ns) 72: Performance: 2989.128 0.008 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (20 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 194.5 72: (ns/day) (hour/ns) 72: Performance: 957.506 0.025 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 2107.627 0.011 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (14 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.015 0.008 198.4 72: (ns/day) (hour/ns) 72: Performance: 188.877 0.127 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.7 72: (ns/day) (hour/ns) 72: Performance: 2786.338 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (88 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.007 0.004 196.6 72: (ns/day) (hour/ns) 72: Performance: 390.010 0.062 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.3 72: (ns/day) (hour/ns) 72: Performance: 2804.094 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (47 ms) 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1216 ms total) 72: 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.2 72: (ns/day) (hour/ns) 72: Performance: 1055.438 0.023 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.8 72: (ns/day) (hour/ns) 72: Performance: 2480.110 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (23 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.3 72: (ns/day) (hour/ns) 72: Performance: 1116.859 0.021 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.0 72: (ns/day) (hour/ns) 72: Performance: 2555.203 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (14 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.4 72: (ns/day) (hour/ns) 72: Performance: 1111.018 0.022 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1600.154 0.015 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (21 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.3 72: (ns/day) (hour/ns) 72: Performance: 1114.838 0.022 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 190.3 72: (ns/day) (hour/ns) 72: Performance: 1589.831 0.015 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1063.822 0.023 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.7 72: (ns/day) (hour/ns) 72: Performance: 2400.855 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.011 0.006 197.3 72: (ns/day) (hour/ns) 72: Performance: 258.827 0.093 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.5 72: (ns/day) (hour/ns) 72: Performance: 2483.109 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (18 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.0 72: (ns/day) (hour/ns) 72: Performance: 999.123 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.6 72: (ns/day) (hour/ns) 72: Performance: 2528.979 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (15 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.015 0.008 197.9 72: (ns/day) (hour/ns) 72: Performance: 195.711 0.123 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.3 72: (ns/day) (hour/ns) 72: Performance: 2531.057 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (28 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.0 72: (ns/day) (hour/ns) 72: Performance: 1125.839 0.021 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.5 72: (ns/day) (hour/ns) 72: Performance: 2412.135 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (18 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 194.6 72: (ns/day) (hour/ns) 72: Performance: 741.347 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 183.7 72: (ns/day) (hour/ns) 72: Performance: 2416.867 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (15 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.1 72: (ns/day) (hour/ns) 72: Performance: 1117.669 0.021 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.0 72: (ns/day) (hour/ns) 72: Performance: 974.315 0.025 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.7 72: (ns/day) (hour/ns) 72: Performance: 738.857 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.0 72: (ns/day) (hour/ns) 72: Performance: 2577.654 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (14 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.237 0.119 199.9 72: (ns/day) (hour/ns) 72: Performance: 12.372 1.940 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 55 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.060 0.030 199.7 72: (ns/day) (hour/ns) 72: Performance: 49.272 0.487 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (170 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.230 0.115 199.9 72: (ns/day) (hour/ns) 72: Performance: 12.761 1.881 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 56 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.059 0.029 199.7 72: (ns/day) (hour/ns) 72: Performance: 49.812 0.482 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (164 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.228 0.114 199.9 72: (ns/day) (hour/ns) 72: Performance: 12.860 1.866 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 56 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.059 0.029 199.7 72: (ns/day) (hour/ns) 72: Performance: 49.955 0.480 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (161 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.199 0.099 199.9 72: (ns/day) (hour/ns) 72: Performance: 14.774 1.625 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.8 72: (ns/day) (hour/ns) 72: Performance: 2544.648 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (115 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 196.5 72: (ns/day) (hour/ns) 72: Performance: 846.352 0.028 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.4 72: (ns/day) (hour/ns) 72: Performance: 2569.055 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (14 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.5 72: (ns/day) (hour/ns) 72: Performance: 753.497 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.4 72: (ns/day) (hour/ns) 72: Performance: 2561.577 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (14 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.011 0.006 198.7 72: (ns/day) (hour/ns) 72: Performance: 266.013 0.090 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 193.0 72: (ns/day) (hour/ns) 72: Performance: 1255.215 0.019 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (25 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 198.8 72: (ns/day) (hour/ns) 72: Performance: 236.618 0.101 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.2 72: (ns/day) (hour/ns) 72: Performance: 2521.733 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 195.7 72: (ns/day) (hour/ns) 72: Performance: 826.482 0.029 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 192.2 72: (ns/day) (hour/ns) 72: Performance: 1478.070 0.016 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 198.8 72: (ns/day) (hour/ns) 72: Performance: 242.105 0.099 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.2 72: (ns/day) (hour/ns) 72: Performance: 2591.752 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (18 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.013 0.006 197.8 72: (ns/day) (hour/ns) 72: Performance: 228.585 0.105 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 56 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.045 0.023 199.5 72: (ns/day) (hour/ns) 72: Performance: 65.112 0.369 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (52 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.2 72: (ns/day) (hour/ns) 72: Performance: 928.220 0.026 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 198.1 72: (ns/day) (hour/ns) 72: Performance: 300.195 0.080 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (40 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.5 72: (ns/day) (hour/ns) 72: Performance: 990.768 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 187.6 72: (ns/day) (hour/ns) 72: Performance: 2048.751 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (40 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.1 72: (ns/day) (hour/ns) 72: Performance: 1017.439 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.1 72: (ns/day) (hour/ns) 72: Performance: 2083.393 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (31 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.2 72: (ns/day) (hour/ns) 72: Performance: 1006.469 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.9 72: (ns/day) (hour/ns) 72: Performance: 2021.192 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (27 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.1 72: (ns/day) (hour/ns) 72: Performance: 1005.483 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 30 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 189.4 72: (ns/day) (hour/ns) 72: Performance: 2052.847 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (28 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.221 0.110 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.298 1.805 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.063 0.032 199.7 72: (ns/day) (hour/ns) 72: Performance: 46.375 0.518 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (172 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.212 0.106 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.835 1.735 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.063 0.031 199.6 72: (ns/day) (hour/ns) 72: Performance: 46.752 0.513 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (166 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.212 0.106 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.872 1.730 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.062 0.031 199.7 72: (ns/day) (hour/ns) 72: Performance: 46.982 0.511 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (165 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.212 0.106 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.834 1.735 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.063 0.031 199.7 72: (ns/day) (hour/ns) 72: Performance: 46.709 0.514 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (166 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.119 0.059 199.7 72: (ns/day) (hour/ns) 72: Performance: 24.735 0.970 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.0 72: (ns/day) (hour/ns) 72: Performance: 2474.134 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (86 ms) 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1934 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 46 tests from 3 test suites ran. (3181 ms total) 72: [ PASSED ] 46 tests. 72/90 Test #72: MdrunNonIntegratorTests ................... Passed 3.20 sec test 73 Start 73: MdrunTpiTests 73: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 3 tests from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 3 tests from Simple/TpiTest 73: [ RUN ] Simple/TpiTest.ReproducesOutput/0 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/0 (163 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/1 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/1 (148 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/2 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/2 (152 ms) 73: [----------] 3 tests from Simple/TpiTest (465 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 3 tests from 1 test suite ran. (472 ms total) 73: [ PASSED ] 3 tests. 73/90 Test #73: MdrunTpiTests ............................. Passed 0.49 sec test 74 Start 74: MdrunMpiTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpiTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 16 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from MimicTest 74: [ RUN ] MimicTest.OneQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.032 0.008 398.6 74: (ns/day) (hour/ns) 74: Performance: 10.850 2.212 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2073968558 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.OneQuantumMol (516 ms) 74: [ RUN ] MimicTest.AllQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 76 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.018 399.4 74: (ns/day) (hour/ns) 74: Performance: 4.712 5.094 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2010119035 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.AllQuantumMol (211 ms) 74: [ RUN ] MimicTest.TwoQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 82 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.224 0.056 399.8 74: (ns/day) (hour/ns) 74: Performance: 1.541 15.572 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -443630233 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.TwoQuantumMol (139 ms) 74: [ RUN ] MimicTest.BondCuts 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 66.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: NVE simulation: will use the initial temperature of 300.368 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 20 % of the run time was spent in domain decomposition, 74: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.000 376.3 74: (ns/day) (hour/ns) 74: Performance: 248.211 0.097 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -17051778 74: 74: Generated 2211 of the 2211 non-bonded parameter combinations 74: 74: Generated 2211 of the 2211 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.BondCuts (63 ms) 74: [----------] 4 tests from MimicTest (931 ms total) 74: 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: There was 1 NOTE 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There was 1 NOTE 74: Setting the LD random seed to -536875033 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -94576705 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -1109393413 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to 975044526 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was turned on during the run due to measured imbalance. 74: Average load imbalance: 48.1%. 74: The balanceable part of the MD step is 7%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 3.4%. 74: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 74: 74: 74: NOTE: 38 % of the run time was spent in domain decomposition, 74: 17 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.104 0.276 399.9 74: (ns/day) (hour/ns) 74: Performance: 6.571 3.653 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (434 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 43 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.004 393.6 74: (ns/day) (hour/ns) 74: Performance: 460.426 0.052 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (27 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 0.1%. 74: The balanceable part of the MD step is 28%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.0%. 74: 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.004 0.251 399.7 74: (ns/day) (hour/ns) 74: Performance: 7.223 3.323 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (10187 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.142 0.285 399.9 74: (ns/day) (hour/ns) 74: Performance: 6.355 3.776 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (5833 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 42 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.248 0.064 387.5 74: (ns/day) (hour/ns) 74: Performance: 28.372 0.846 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (154 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.749 0.437 399.9 74: (ns/day) (hour/ns) 74: Performance: 4.148 5.786 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (489 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (17128 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 16 tests from 2 test suites ran. (18089 ms total) 74: [ PASSED ] 10 tests. 74: [ SKIPPED ] 6 tests, listed below: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74/90 Test #74: MdrunMpiTests ............................. Passed 18.10 sec test 75 Start 75: MdrunMultiSimTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 2 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 2 tests from InNvt/MultiSimTerminationTest 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 75: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 2 tests from 1 test suite ran. (7 ms total) 75: [ PASSED ] 2 tests. 75: 75: YOU HAVE 4 DISABLED TESTS 75: 75/90 Test #75: MdrunMultiSimTests ........................ Passed 0.02 sec test 76 Start 76: MdrunMultiSimReplexTests 76: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 1 test from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 76: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 76: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 1 test from 1 test suite ran. (7 ms total) 76: [ PASSED ] 1 test. 76: 76: YOU HAVE 4 DISABLED TESTS 76: 76/90 Test #76: MdrunMultiSimReplexTests .................. Passed 0.02 sec test 77 Start 77: MdrunMultiSimReplexEquivalenceTests 77: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 0 tests from 0 test suites. 77: [==========] 0 tests from 0 test suites ran. (0 ms total) 77: [ PASSED ] 0 tests. 77: 77: YOU HAVE 10 DISABLED TESTS 77: 77/90 Test #77: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.02 sec test 78 Start 78: MdrunMpi1RankPmeTests 78: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -68185677 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to 2041303006 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.011 199.3 78: (ns/day) (hour/ns) 78: Performance: 157.792 0.152 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (9831 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 199.3 78: (ns/day) (hour/ns) 78: Performance: 169.759 0.141 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (14 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.003 0.001 190.3 78: (ns/day) (hour/ns) 78: Performance: 64.979 0.369 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (30971 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.020 0.010 198.8 78: (ns/day) (hour/ns) 78: Performance: 181.865 0.132 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (15 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (40834 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (40848 ms total) 78: [ PASSED ] 4 tests. 78: [ SKIPPED ] 15 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78/90 Test #78: MdrunMpi1RankPmeTests ..................... Passed 40.86 sec test 79 Start 79: MdrunMpi2RankPmeTests 79: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 19 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 19 tests from ReproducesEnergies/PmeTest 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 13.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 966.268 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -270664347 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -175899203 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Searching the wall atom type(s) 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was turned on during the run due to measured imbalance. 79: Average load imbalance: 31.5%. 79: The balanceable part of the MD step is 17%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 5.3%. 79: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 79: 79: NOTE: 5.3 % of the available CPU time was lost due to load imbalance 79: in the domain decomposition. 79: You can consider manually changing the decomposition (option -dd); 79: e.g. by using fewer domains along the box dimension in which there is 79: considerable inhomogeneity in the simulated system. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 4.779 1.195 400.0 79: (ns/day) (hour/ns) 79: Performance: 1.519 15.805 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (11113 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was turned on during the run due to measured imbalance. 79: Average load imbalance: 9.8%. 79: The balanceable part of the MD step is 22%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 2.2%. 79: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 79: 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.909 0.227 399.9 79: (ns/day) (hour/ns) 79: Performance: 7.985 3.006 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (250 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 39 % of the run time was spent in domain decomposition, 79: 6 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.114 0.029 393.3 79: (ns/day) (hour/ns) 79: Performance: 2.971 8.078 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (30487 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.694 0.423 399.9 79: (ns/day) (hour/ns) 79: Performance: 4.284 5.602 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (5735 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.288 0.322 399.9 79: (ns/day) (hour/ns) 79: Performance: 5.634 4.260 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (384 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 24 % of the run time was spent in domain decomposition, 79: 8 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.049 0.012 390.1 79: (ns/day) (hour/ns) 79: Performance: 6.933 3.461 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (19313 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was turned on during the run due to measured imbalance. 79: Average load imbalance: 19.2%. 79: The balanceable part of the MD step is 27%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 5.1%. 79: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 79: 79: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 79: in the domain decomposition. 79: You can consider manually changing the decomposition (option -dd); 79: e.g. by using fewer domains along the box dimension in which there is 79: considerable inhomogeneity in the simulated system. 79: 79: NOTE: 10 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 5.443 1.361 400.0 79: (ns/day) (hour/ns) 79: Performance: 1.333 18.001 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (1497 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [----------] 19 tests from ReproducesEnergies/PmeTest (68784 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 19 tests from 1 test suite ran. (68797 ms total) 79: [ PASSED ] 7 tests. 79: [ SKIPPED ] 12 tests, listed below: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79/90 Test #79: MdrunMpi2RankPmeTests ..................... Passed 68.81 sec test 80 Start 80: MdrunCoordinationBasicTests1Rank 80: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.002 98.2 80: (ns/day) (hour/ns) 80: Performance: 819.555 0.029 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 96.7 80: (ns/day) (hour/ns) 80: Performance: 1799.239 0.013 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.5 80: (ns/day) (hour/ns) 80: Performance: 2694.923 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.7 80: (ns/day) (hour/ns) 80: Performance: 2548.860 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.4 80: (ns/day) (hour/ns) 80: Performance: 2574.423 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.8 80: (ns/day) (hour/ns) 80: Performance: 2571.199 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (27 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (27 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (35 ms total) 80: [ PASSED ] 1 test. 80/90 Test #80: MdrunCoordinationBasicTests1Rank .......... Passed 0.05 sec test 81 Start 81: MdrunCoordinationBasicTests2Ranks 81: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 1 test from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest 81: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.5%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.3%. 81: 81: 81: NOTE: 37 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 195.1 81: (ns/day) (hour/ns) 81: Performance: 775.112 0.031 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.1%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.0%. 81: 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.002 0.001 191.5 81: (ns/day) (hour/ns) 81: Performance: 1753.656 0.014 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.4%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.6%. 81: 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 190.4 81: (ns/day) (hour/ns) 81: Performance: 2017.552 0.012 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.0%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 190.6 81: (ns/day) (hour/ns) 81: Performance: 1933.949 0.012 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.1%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.5%. 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 190.3 81: (ns/day) (hour/ns) 81: Performance: 1943.098 0.012 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.8%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.8%. 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 189.9 81: (ns/day) (hour/ns) 81: Performance: 1908.486 0.013 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (116 ms) 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest (117 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 1 test from 1 test suite ran. (124 ms total) 81: [ PASSED ] 1 test. 81/90 Test #81: MdrunCoordinationBasicTests2Ranks ......... Passed 0.14 sec test 82 Start 82: MdrunCoordinationCouplingTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 98.2 82: (ns/day) (hour/ns) 82: Performance: 943.863 0.025 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2424.476 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2710.336 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 61.1 82: (ns/day) (hour/ns) 82: Performance: 1631.513 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1400.453 0.017 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2645.167 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (28 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2049.432 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2335.327 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2734.396 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2477.119 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.8 82: (ns/day) (hour/ns) 82: Performance: 2371.283 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1734.890 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1965.102 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2314.273 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2766.320 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.8 82: (ns/day) (hour/ns) 82: Performance: 2563.709 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.6 82: (ns/day) (hour/ns) 82: Performance: 2734.396 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2632.732 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (29 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2139.095 0.011 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2416.867 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2672.709 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2560.513 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 71.6 82: (ns/day) (hour/ns) 82: Performance: 1846.147 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1785.679 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1990.499 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2491.142 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2862.729 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2569.055 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2749.038 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2757.652 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2038.582 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2479.112 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1880.523 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2548.860 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2614.853 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2649.718 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2075.672 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2488.123 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2842.914 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2599.407 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2566.914 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2697.283 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1611.877 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1781.033 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2824.665 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2632.732 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2638.370 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2703.200 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 2222.436 0.011 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2662.314 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2868.060 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2588.485 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 1878.230 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1903.768 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2091.882 0.011 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2499.227 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2802.818 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2733.183 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2656.573 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2614.853 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2012.608 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1774.876 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2832.457 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2575.499 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2557.324 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2547.806 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2167.697 0.011 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2518.640 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2365.819 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2151.045 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.005 0.005 99.2 82: (ns/day) (hour/ns) 82: Performance: 301.502 0.080 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2595.027 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (31 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 2005.402 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2371.283 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2923.870 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2622.645 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2625.999 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2665.770 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 2011.951 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1842.834 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2671.550 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2523.799 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2585.226 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2385.054 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 2082.689 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 2371.283 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2775.042 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2398.985 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2497.201 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2406.482 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 2020.529 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2369.459 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2651.999 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2518.640 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1916.203 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2390.607 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.7 82: (ns/day) (hour/ns) 82: Performance: 1697.133 0.014 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1846.701 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1997.598 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 2014.583 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1889.173 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.6 82: (ns/day) (hour/ns) 82: Performance: 1537.458 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1554.920 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1801.870 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1935.468 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1840.632 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1817.821 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.6 82: (ns/day) (hour/ns) 82: Performance: 1883.974 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (29 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.8 82: (ns/day) (hour/ns) 82: Performance: 1484.480 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.5 82: (ns/day) (hour/ns) 82: Performance: 1846.147 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 2021.856 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1495.653 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1440.401 0.017 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1811.939 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1641.075 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1773.343 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2103.310 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 2025.179 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 1538.226 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1543.622 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1521.886 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1797.664 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 1956.987 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1783.611 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.9 82: (ns/day) (hour/ns) 82: Performance: 1479.489 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1793.477 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (29 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.0 82: (ns/day) (hour/ns) 82: Performance: 1522.262 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 1619.930 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1926.992 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 1739.789 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1888.594 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1816.748 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (28 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1345.108 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.1 82: (ns/day) (hour/ns) 82: Performance: 1200.895 0.020 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.1 82: (ns/day) (hour/ns) 82: Performance: 1641.949 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.0 82: (ns/day) (hour/ns) 82: Performance: 1554.528 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1559.249 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1540.148 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (29 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 97.2 82: (ns/day) (hour/ns) 82: Performance: 787.095 0.030 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1196.464 0.020 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.0 82: (ns/day) (hour/ns) 82: Performance: 1235.083 0.019 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 97.4 82: (ns/day) (hour/ns) 82: Performance: 791.138 0.030 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1182.683 0.020 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1166.779 0.021 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (31 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.9 82: (ns/day) (hour/ns) 82: Performance: 1138.952 0.021 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1408.780 0.017 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1600.570 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1517.388 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1539.379 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 97.5 82: (ns/day) (hour/ns) 82: Performance: 934.556 0.026 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (29 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (696 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (705 ms total) 82: [ PASSED ] 25 tests. 82/90 Test #82: MdrunCoordinationCouplingTests1Rank ....... Passed 0.72 sec test 83 Start 83: MdrunCoordinationCouplingTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 25 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 53%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 37 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 195.1 83: (ns/day) (hour/ns) 83: Performance: 826.537 0.029 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.2 83: (ns/day) (hour/ns) 83: Performance: 1799.502 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.3%. 83: The balanceable part of the MD step is 38%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 2040.269 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 37%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 2001.818 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.7%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 2040.269 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.5%. 83: The balanceable part of the MD step is 37%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1966.670 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (138 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.9 83: (ns/day) (hour/ns) 83: Performance: 1528.304 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.8 83: (ns/day) (hour/ns) 83: Performance: 1737.336 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.8 83: (ns/day) (hour/ns) 83: Performance: 1956.055 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1925.186 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1895.859 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.6%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1888.305 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (414 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.1 83: (ns/day) (hour/ns) 83: Performance: 1471.890 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1764.707 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1981.217 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1850.028 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1851.975 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 40%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1828.612 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (139 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.5%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 24 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.9 83: (ns/day) (hour/ns) 83: Performance: 1533.630 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.6%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1760.421 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1921.882 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.6%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1836.243 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1859.521 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.5%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1905.240 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (604 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1709.140 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1952.335 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 2215.642 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 1982.173 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2048.410 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2056.616 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (116 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.5 83: (ns/day) (hour/ns) 83: Performance: 1597.664 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1860.925 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.0 83: (ns/day) (hour/ns) 83: Performance: 2062.123 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1964.475 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1979.943 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 1906.714 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (48 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1580.450 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.8 83: (ns/day) (hour/ns) 83: Performance: 1845.042 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 2085.862 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 1984.088 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 32 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 187.7 83: (ns/day) (hour/ns) 83: Performance: 1947.398 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.3 83: (ns/day) (hour/ns) 83: Performance: 2076.021 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (739 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1652.520 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.5 83: (ns/day) (hour/ns) 83: Performance: 1803.981 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.3 83: (ns/day) (hour/ns) 83: Performance: 2048.070 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1972.968 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1962.285 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 1971.390 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (92 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.4 83: (ns/day) (hour/ns) 83: Performance: 1644.140 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1964.788 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 81 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.069 0.035 199.7 83: (ns/day) (hour/ns) 83: Performance: 42.261 0.568 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 2111.962 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 2071.136 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2046.029 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (731 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1605.576 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1880.236 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2091.172 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 1980.898 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 2006.055 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 2032.864 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (104 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.7 83: (ns/day) (hour/ns) 83: Performance: 1638.456 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1834.602 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2147.297 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 2082.337 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2090.817 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 2078.122 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (539 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1721.558 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1954.503 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 2145.801 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 1994.365 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 2048.751 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 1997.598 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (363 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.1 83: (ns/day) (hour/ns) 83: Performance: 1667.278 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 191.1 83: (ns/day) (hour/ns) 83: Performance: 1982.173 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 2283.816 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 2190.433 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 2178.428 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 2177.658 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (84 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.9 83: (ns/day) (hour/ns) 83: Performance: 1643.482 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 191.2 83: (ns/day) (hour/ns) 83: Performance: 1874.800 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 2059.022 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1995.011 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1991.142 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1996.304 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (107 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.4 83: (ns/day) (hour/ns) 83: Performance: 1657.633 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1745.953 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 2184.608 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.8 83: (ns/day) (hour/ns) 83: Performance: 2106.546 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 2006.055 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1993.075 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (687 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.1 83: (ns/day) (hour/ns) 83: Performance: 1660.314 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1912.040 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 2118.863 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 2107.627 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1987.609 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1885.415 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (116 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.3 83: (ns/day) (hour/ns) 83: Performance: 1117.771 0.021 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 55%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.794 0.397 200.0 83: (ns/day) (hour/ns) 83: Performance: 3.699 6.488 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1356.511 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.6%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 1297.377 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.6%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1326.000 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 1273.245 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (803 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.1 83: (ns/day) (hour/ns) 83: Performance: 1020.304 0.024 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1196.929 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1243.936 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1197.394 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.461 0.231 199.9 83: (ns/day) (hour/ns) 83: Performance: 6.371 3.767 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1210.333 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (652 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 56%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1011.011 0.024 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1200.311 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.6%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1254.703 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.8 83: (ns/day) (hour/ns) 83: Performance: 1253.810 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 1208.433 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1183.364 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (75 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1164.023 0.021 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1315.523 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 187.9 83: (ns/day) (hour/ns) 83: Performance: 1506.074 0.016 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.1 83: (ns/day) (hour/ns) 83: Performance: 1410.554 0.017 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1438.383 0.017 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.1 83: (ns/day) (hour/ns) 83: Performance: 1382.539 0.017 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (625 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1145.837 0.021 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1287.750 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.0 83: (ns/day) (hour/ns) 83: Performance: 1355.317 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 1320.033 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 23 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 191.1 83: (ns/day) (hour/ns) 83: Performance: 960.567 0.025 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 187.9 83: (ns/day) (hour/ns) 83: Performance: 1292.749 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (94 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 1089.696 0.022 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1251.263 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.1 83: (ns/day) (hour/ns) 83: Performance: 1332.020 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 1215.947 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1271.012 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 1235.207 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (116 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1006.551 0.024 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1107.323 0.022 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 1157.136 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1145.305 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1132.879 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1164.023 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (123 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.7 83: (ns/day) (hour/ns) 83: Performance: 843.339 0.028 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.8 83: (ns/day) (hour/ns) 83: Performance: 890.710 0.027 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.1 83: (ns/day) (hour/ns) 83: Performance: 947.201 0.025 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.2 83: (ns/day) (hour/ns) 83: Performance: 932.223 0.026 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.2 83: (ns/day) (hour/ns) 83: Performance: 904.108 0.027 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.2 83: (ns/day) (hour/ns) 83: Performance: 942.563 0.025 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (92 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.5 83: (ns/day) (hour/ns) 83: Performance: 975.395 0.025 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 190.4 83: (ns/day) (hour/ns) 83: Performance: 1086.141 0.022 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1205.596 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1074.960 0.022 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1135.070 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1160.952 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (583 ms) 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (8197 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 25 tests from 1 test suite ran. (8204 ms total) 83: [ PASSED ] 25 tests. 83/90 Test #83: MdrunCoordinationCouplingTests2Ranks ...... Passed 8.22 sec test 84 Start 84: MdrunCoordinationConstraintsTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1965.102 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2254.151 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2550.970 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2472.148 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 1896.151 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2442.741 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (854 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1855.601 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2225.648 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2446.622 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 91.8 84: (ns/day) (hour/ns) 84: Performance: 2272.443 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2355.868 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2265.757 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (826 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1899.659 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2228.869 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2429.256 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2264.092 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2350.475 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2272.443 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (830 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1956.987 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2301.305 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2519.670 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 1875.942 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2352.269 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 1864.586 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (826 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1929.406 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1751.164 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2490.135 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2257.455 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2314.273 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 1813.006 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (824 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1909.669 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2202.572 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.5 84: (ns/day) (hour/ns) 84: Performance: 2402.728 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2356.769 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 1856.160 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2245.114 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (834 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1840.082 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1762.184 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: NOTE: 17 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1946.475 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1747.686 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1714.610 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2260.768 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (835 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1829.698 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1981.535 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2228.063 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2201.785 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2000.842 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2126.543 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (827 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1818.357 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 2050.797 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2196.290 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2130.219 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2125.075 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2095.440 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (834 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1290.717 0.019 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1205.832 0.020 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1713.656 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1683.222 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1642.825 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1668.633 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (849 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1356.361 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1558.066 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1657.410 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1374.212 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1596.422 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1583.293 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (837 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1239.556 0.019 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1664.126 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1664.126 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1444.453 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1735.867 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1640.637 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (832 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1422.770 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1604.321 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1729.532 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1341.885 0.018 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1351.304 0.018 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1313.559 0.018 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (838 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (10849 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (10861 ms total) 84: [ PASSED ] 13 tests. 84/90 Test #84: MdrunCoordinationConstraintsTests1Rank .... Passed 10.88 sec test 85 Start 85: MdrunCoordinationConstraintsTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 13 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.5%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.2 85: (ns/day) (hour/ns) 85: Performance: 1429.538 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1689.686 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 6 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 1960.724 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1837.886 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1816.481 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1874.230 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (952 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 23 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.6 85: (ns/day) (hour/ns) 85: Performance: 1360.405 0.018 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1490.226 0.016 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1888.884 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1691.774 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1757.408 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.4%. 85: The balanceable part of the MD step is 1%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.0%. 85: 85: 85: NOTE: 97 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 199.6 85: (ns/day) (hour/ns) 85: Performance: 54.479 0.441 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2013 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 23 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.5 85: (ns/day) (hour/ns) 85: Performance: 1390.967 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1611.666 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1871.952 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.5%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1747.438 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 12 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1741.264 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1771.049 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1373 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.1 85: (ns/day) (hour/ns) 85: Performance: 1485.554 0.016 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1859.241 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 2052.163 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1856.999 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1867.696 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1899.073 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1381 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.8 85: (ns/day) (hour/ns) 85: Performance: 1440.738 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1721.077 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1927.595 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1738.071 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1796.091 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1800.553 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (907 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1431.864 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1715.326 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1757.408 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.5 85: (ns/day) (hour/ns) 85: Performance: 1776.923 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1751.911 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1742.989 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1408 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.4 85: (ns/day) (hour/ns) 85: Performance: 1402.685 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.5 85: (ns/day) (hour/ns) 85: Performance: 1662.105 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1888.015 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.6 85: (ns/day) (hour/ns) 85: Performance: 1745.211 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1790.350 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1696.900 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (943 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.2 85: (ns/day) (hour/ns) 85: Performance: 1391.596 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.8 85: (ns/day) (hour/ns) 85: Performance: 1614.200 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1694.333 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1654.295 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1631.297 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1669.538 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (928 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.8 85: (ns/day) (hour/ns) 85: Performance: 1343.055 0.018 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1550.810 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1675.212 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1622.276 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1630.865 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1561.621 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1898 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.4%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 191.9 85: (ns/day) (hour/ns) 85: Performance: 981.064 0.024 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.4%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.350 0.175 199.9 85: (ns/day) (hour/ns) 85: Performance: 8.383 2.863 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1308.676 0.018 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1272.061 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1218.110 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1262.675 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1457 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 191.7 85: (ns/day) (hour/ns) 85: Performance: 963.345 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1114.031 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1188.501 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1115.847 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1125.223 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.6 85: (ns/day) (hour/ns) 85: Performance: 1100.794 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (924 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.0 85: (ns/day) (hour/ns) 85: Performance: 951.370 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1104.049 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1250.882 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1177.484 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.7 85: (ns/day) (hour/ns) 85: Performance: 1185.413 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1192.873 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (920 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 188.8 85: (ns/day) (hour/ns) 85: Performance: 971.702 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1094.244 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1163.584 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1089.310 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1057.522 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1099.027 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1192 ms) 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (16301 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 13 tests from 1 test suite ran. (16309 ms total) 85: [ PASSED ] 13 tests. 85/90 Test #85: MdrunCoordinationConstraintsTests2Ranks ... Passed 16.33 sec test 86 Start 86: MdrunFEPTests 86: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunFEPTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 14 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 2 tests from ExpandedEnsembleTest 86: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 16 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.007 0.004 197.5 86: (ns/day) (hour/ns) 86: Performance: 392.220 0.061 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.004 0.002 191.6 86: (ns/day) (hour/ns) 86: Performance: 344.366 0.070 86: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (35 ms) 86: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 1 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 16 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.042 0.021 199.6 86: (ns/day) (hour/ns) 86: Performance: 8.213 2.922 86: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (39 ms) 86: [----------] 2 tests from ExpandedEnsembleTest (74 ms total) 86: 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -343957505 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.845 0.423 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.293 5.591 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10359 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1687753137 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 19 % of the run time was spent in domain decomposition, 86: 8 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.080 0.040 199.7 86: (ns/day) (hour/ns) 86: Performance: 45.074 0.532 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (136 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1327109 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.038 0.019 199.5 86: (ns/day) (hour/ns) 86: Performance: 95.658 0.251 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (100 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 155]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 155]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to 1465840111 86: 86: Generated 171 of the 171 non-bonded parameter combinations 86: 86: Generated 171 of the 171 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 358.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 1 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.96 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.054 0.027 199.5 86: (ns/day) (hour/ns) 86: Performance: 67.269 0.357 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (12427 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 165]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 165]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to -1052369 86: 86: Generated 190 of the 190 non-bonded parameter combinations 86: 86: Generated 190 of the 190 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'CL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'CL' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 361.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 2 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.96 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.049 0.025 199.4 86: (ns/day) (hour/ns) 86: Performance: 73.287 0.327 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (39 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 86: and vdw_modifier=Force-switch 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 100 steps, 0.1 ps. 86: Setting the LD random seed to -1360011346 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.230 0.115 199.9 86: (ns/day) (hour/ns) 86: Performance: 75.889 0.316 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (189 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There were 11 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to 2143928251 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.072 0.036 199.7 86: (ns/day) (hour/ns) 86: Performance: 50.285 0.477 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (113 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: Removing center of mass motion in the presence of position restraints 86: might cause artifacts. When you are using position restraints to 86: equilibrate a macro-molecule, the artifacts are usually negligible. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 11 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -84484114 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.072 0.036 199.7 86: (ns/day) (hour/ns) 86: Performance: 50.143 0.479 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (113 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1618134313 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.89 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.015 199.1 86: (ns/day) (hour/ns) 86: Performance: 119.257 0.201 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (91 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.017 0.009 198.6 86: (ns/day) (hour/ns) 86: Performance: 210.609 0.114 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -1140852481 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.90 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (92 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1092837924 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.067 0.034 199.7 86: (ns/day) (hour/ns) 86: Performance: 54.110 0.444 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (108 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to 1576523434 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.90 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.015 199.3 86: (ns/day) (hour/ns) 86: Performance: 120.631 0.199 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (91 ms) 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (23864 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 14 tests from 2 test suites ran. (23954 ms total) 86: [ PASSED ] 14 tests. 86/90 Test #86: MdrunFEPTests ............................. Passed 23.97 sec test 87 Start 87: MdrunPullTests 87: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunPullTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 4 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from PullTest/PullIntegrationTest 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.600 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 14 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.059 0.029 199.6 87: (ns/day) (hour/ns) 87: Performance: 61.706 0.389 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (191 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.301 nm 0.400 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.090 0.045 199.7 87: (ns/day) (hour/ns) 87: Performance: 40.334 0.595 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (206 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Pull group 3 'r_3' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1292.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.357 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.500 nm 87: 1 3 2 87: 3 3 8 0.331 nm 0.400 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.040 0.020 199.5 87: (ns/day) (hour/ns) 87: Performance: 89.441 0.268 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (179 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.000 nm 87: 1 3 2 87: 2 3 5 0.050 nm 0.000 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.040 0.020 199.4 87: (ns/day) (hour/ns) 87: Performance: 89.696 0.268 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (180 ms) 87: [----------] 4 tests from PullTest/PullIntegrationTest (757 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 4 tests from 1 test suite ran. (765 ms total) 87: [ PASSED ] 4 tests. 87/90 Test #87: MdrunPullTests ............................ Passed 0.78 sec test 88 Start 88: MdrunRotationTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunRotationTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 12 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 12 tests from RotationWorks/RotationTest 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 88: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: trr version: GMX_trn_file (single precision) 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -296321 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.003 0.002 195.1 88: (ns/day) (hour/ns) 88: Performance: 2822.674 0.009 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (17 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 88: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2141052891 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.010 0.005 198.3 88: (ns/day) (hour/ns) 88: Performance: 871.125 0.028 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (10 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 88: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 486864383 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.012 0.006 197.8 88: (ns/day) (hour/ns) 88: Performance: 752.022 0.032 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (14 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 88: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1585290735 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 192.3 88: (ns/day) (hour/ns) 88: Performance: 5345.864 0.004 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (5 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 88: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -42092809 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 191.8 88: (ns/day) (hour/ns) 88: Performance: 4764.645 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (15 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 88: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -302121986 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.015 0.008 198.3 88: (ns/day) (hour/ns) 88: Performance: 586.973 0.041 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (15 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 88: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1218707714 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.013 0.007 198.2 88: (ns/day) (hour/ns) 88: Performance: 667.286 0.036 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (12 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 88: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -470291725 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.013 0.006 197.9 88: (ns/day) (hour/ns) 88: Performance: 707.125 0.034 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (11 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 88: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -17603086 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.016 0.008 199.1 88: (ns/day) (hour/ns) 88: Performance: 560.772 0.043 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (13 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 88: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1229087809 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.012 0.006 198.8 88: (ns/day) (hour/ns) 88: Performance: 749.957 0.032 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (10 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 88: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -147865633 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.007 0.004 196.9 88: (ns/day) (hour/ns) 88: Performance: 1231.887 0.019 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (14 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 88: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1879220737 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: NOTE: 19 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.182 0.091 199.9 88: (ns/day) (hour/ns) 88: Performance: 49.211 0.488 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (99 ms) 88: [----------] 12 tests from RotationWorks/RotationTest (242 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 12 tests from 1 test suite ran. (250 ms total) 88: [ PASSED ] 12 tests. 88/90 Test #88: MdrunRotationTests ........................ Passed 0.26 sec test 89 Start 89: MdrunSimulatorComparison 89: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 0 tests from 0 test suites. 89: [==========] 0 tests from 0 test suites ran. (0 ms total) 89: [ PASSED ] 0 tests. 89: 89: YOU HAVE 82 DISABLED TESTS 89: 89/90 Test #89: MdrunSimulatorComparison .................. Passed 0.01 sec test 90 Start 90: MdrunVirtualSiteTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 37 tests from 2 test suites. 90: [----------] Global test environment set-up. 90: [----------] 1 test from VirtualSiteVelocityTest 90: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 90: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 90: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 90: 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.8%. 90: The balanceable part of the MD step is 39%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.7%. 90: 90: 90: NOTE: 38 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.003 0.002 194.1 90: (ns/day) (hour/ns) 90: Performance: 475.817 0.050 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: trr version: GMX_trn_file (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (389 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.5%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 1.0%. 90: 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.7 90: (ns/day) (hour/ns) 90: Performance: 879.464 0.027 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (19 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.8%. 90: The balanceable part of the MD step is 35%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.6%. 90: 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.0 90: (ns/day) (hour/ns) 90: Performance: 964.795 0.025 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (119 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.5 90: (ns/day) (hour/ns) 90: Performance: 1023.534 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (29 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.5 90: (ns/day) (hour/ns) 90: Performance: 1051.585 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (22 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.8 90: (ns/day) (hour/ns) 90: Performance: 987.732 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (17 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.5 90: (ns/day) (hour/ns) 90: Performance: 1060.820 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (39 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.4 90: (ns/day) (hour/ns) 90: Performance: 1032.281 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (20 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.6 90: (ns/day) (hour/ns) 90: Performance: 1048.037 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (15 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.6%. 90: The balanceable part of the MD step is 39%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.6%. 90: 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 190.2 90: (ns/day) (hour/ns) 90: Performance: 911.158 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (13 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.3%. 90: The balanceable part of the MD step is 41%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.5%. 90: 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.5 90: (ns/day) (hour/ns) 90: Performance: 846.151 0.028 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.2 90: (ns/day) (hour/ns) 90: Performance: 979.133 0.025 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (35 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.1 90: (ns/day) (hour/ns) 90: Performance: 938.964 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (18 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.7 90: (ns/day) (hour/ns) 90: Performance: 912.178 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (26 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.5 90: (ns/day) (hour/ns) 90: Performance: 911.158 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (25 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 8 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.006 0.003 197.2 90: (ns/day) (hour/ns) 90: Performance: 258.264 0.093 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (670 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.7 90: (ns/day) (hour/ns) 90: Performance: 987.283 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (37 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.8 90: (ns/day) (hour/ns) 90: Performance: 985.047 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (30 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 189.7 90: (ns/day) (hour/ns) 90: Performance: 1051.077 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (24 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.5 90: (ns/day) (hour/ns) 90: Performance: 1021.130 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (21 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 189.1 90: (ns/day) (hour/ns) 90: Performance: 1053.623 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (63 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1674 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 37 tests from 2 test suites ran. (1682 ms total) 90: [ PASSED ] 37 tests. 90/90 Test #90: MdrunVirtualSiteTests ..................... Passed 1.70 sec 100% tests passed, 0 tests failed out of 90 Label Time Summary: GTest = 909.71 sec*proc (88 tests) IntegrationTest = 829.16 sec*proc (28 tests) MpiTest = 706.49 sec*proc (21 tests) QuickGpuTest = 97.41 sec*proc (22 tests) SlowGpuTest = 792.91 sec*proc (14 tests) SlowTest = 73.74 sec*proc (14 tests) UnitTest = 6.81 sec*proc (46 tests) Total Test time (real) = 343.22 sec /usr/bin/make -j12 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 77 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend [ 0%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 0%] Built target internal_rpc_xdr make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 2%] Built target thread_mpi make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build [ 2%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" [ 3%] Built target linearalgebra make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 5%] Built target options /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 7%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 7%] Built target energyanalysis [ 9%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 9%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 10%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 61%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 62%] Built target gmxapi [ 63%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build [ 63%] Built target argon-forces-integration make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 63%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 63%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 63%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/interactivetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/loggertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpi_printer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stdiohelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stringtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfilemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_device.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_hardware_environment.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/textblockmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o -MF CMakeFiles/testutils.dir/topologyhelpers.cpp.o.d -o CMakeFiles/testutils.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tprfilegenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o -MF CMakeFiles/testutils.dir/trajectoryreader.cpp.o.d -o CMakeFiles/testutils.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/xvgtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/topologyhelpers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energyreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energycomparison.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/testsystems.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/interactivetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/naming.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/mpitest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/refdata_tests.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target testutils-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/mock_helptopic.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target domdec-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energydrifttracker.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target fft-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/complex.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/observablesreducer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 68%] Built target awh-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extensions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/expanded.cpp [ 70%] Built target nbnxm-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target listed_forces-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target hardware-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoption.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 72%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/dofit.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 72%] Built target mdspan-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreeserializer.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target pbcutil-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target timing-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestrunners.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/path.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target pull-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/threefry.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 75%] Built target ewald-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 75%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 76%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 76%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/repeatingsection.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target random-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genconf.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 79%] Built target topology-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 79%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target mdlib-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadapters.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target correlations-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/dump.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/make_ndx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/checkpoint.cpp [ 81%] Built target utility-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/requirements.cpp [ 81%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 81%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 81%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filemd5.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 81%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 83%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multiple_time_stepping.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 83%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 84%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/constantacceleration.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 84%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 84%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 84%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 85%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/grompp.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisim.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 87%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 87%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/tngio.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 88%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectionoption.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 89%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 90%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 90%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 90%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" [ 93%] Built target mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/tpr.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 [ 93%] Built target mdrun-pull-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/setup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target selection-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" [ 94%] Built target nblib-integrator-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/analysisdata.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/pbcholder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/virials.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/select.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/unionfind.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -537166085 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 191.4 1: (ns/day) (hour/ns) 1: Performance: 529.782 0.045 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (278 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -537265057 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 189.9 1: (ns/day) (hour/ns) 1: Performance: 623.419 0.038 1: [ OK ] GmxApiTest.RunnerBasicMD (296 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -350224388 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.015 0.008 198.1 1: (ns/day) (hour/ns) 1: Performance: 459.248 0.052 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 192.4 1: (ns/day) (hour/ns) 1: Performance: 3268.873 0.007 1: [ OK ] GmxApiTest.RunnerReinitialize (305 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 377481086 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.014 0.007 197.9 1: (ns/day) (hour/ns) 1: Performance: 70.895 0.339 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 190.7 1: (ns/day) (hour/ns) 1: Performance: 809.210 0.030 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (309 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -142607057 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.015 0.008 198.1 1: (ns/day) (hour/ns) 1: Performance: 109.793 0.219 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 187.9 1: (ns/day) (hour/ns) 1: Performance: 559.517 0.043 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (312 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -939614373 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (281 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1784 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1797 ms total) 1: [ PASSED ] 9 tests. 1/90 Test #1: GmxapiExternalInterfaceTests .............. Passed 1.83 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2097086357 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (247 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1090866697 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (254 ms) 2: [----------] 2 tests from GmxApiTest (501 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (509 ms total) 2: [ PASSED ] 2 tests. 2/90 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.53 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (12 ms) 3: [----------] 8 tests from NBlibTest (14 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (6 ms) 3: [----------] 1 test from LinearChainDataFixture (6 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (21 ms total) 3: [ PASSED ] 44 tests. 3/90 Test #3: NbLibListedForcesTests .................... Passed 0.04 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/90 Test #4: NbLibSamplesTestArgon ..................... Passed 0.02 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/90 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.07 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/90 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (1 ms total) 7: [ PASSED ] 57 tests. 7/90 Test #7: NbLibSetupTests ........................... Passed 0.07 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (10 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (19 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (5 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (11 ms) 8: [----------] 4 tests from TprReaderTest (46 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (62 ms total) 8: [ PASSED ] 4 tests. 8/90 Test #8: NbLibTprTests ............................. Passed 0.09 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (20 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (23 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (23 ms total) 9: [ PASSED ] 20 tests. 9/90 Test #9: NbLibIntegrationTests ..................... Passed 0.06 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/90 Test #10: NbLibIntegratorTests ...................... Passed 0.03 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (16 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (18 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (20 ms total) 11: [ PASSED ] 75 tests. 11/90 Test #11: TestUtilsUnitTests ........................ Passed 0.05 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (6 ms) 12: [----------] 1 test from MpiSelfTest (6 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (6 ms total) 12: [ PASSED ] 1 test. 12/90 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.02 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (0 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (0 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (0 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (4 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/90 Test #13: UtilityUnitTests .......................... Passed 0.06 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (25 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (4 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (29 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (29 ms total) 14: [ PASSED ] 2 tests. 14/90 Test #14: UtilityMpiUnitTests ....................... Passed 0.04 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (6 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (6 ms total) 15: [ PASSED ] 78 tests. 15/90 Test #15: GmxlibTests ............................... Passed 0.03 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (0 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (0 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (0 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (6 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (6 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (15 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (4 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (19 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (8 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (18 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (5 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (9 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (4 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (4 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (96 ms total) 16: [ PASSED ] 1032 tests. 16/90 Test #16: MdlibUnitTest ............................. Passed 0.19 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (0 ms) 17: [----------] 1 test from BiasTest (0 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (1 ms) 17: [----------] 1 test from biasGridTest (1 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (43 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (439 ms) 17: [----------] 2 tests from BiasSharingTest (483 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (4 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (9 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (22 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (14 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (527 ms total) 17: [ PASSED ] 27 tests. 17/90 Test #17: AwhTest ................................... Passed 0.54 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (0 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (1 ms total) 18: [ PASSED ] 18 tests. 18/90 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.02 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -111175206 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -420348421 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1949640257 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -808526051 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (8 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to 1610452825 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (8 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1450616 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (2 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (28 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (0 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (29 ms total) 19: [ PASSED ] 21 tests. 19/90 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.05 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to 1929297307 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (6 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (7 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to 1070313326 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -1222911169 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -93651073 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to 854839807 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (14 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -944251395 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -1627389955 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -194049137 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (25 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to 870069695 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (31 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (63 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (85 ms total) 20: [ PASSED ] 16 tests. 20/90 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.11 sec test 21 Start 21: NNPotAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 21: Test timeout computed to be: 30 21: [==========] Running 12 tests from 4 test suites. 21: [----------] Global test environment set-up. 21: [----------] 1 test from NNPotTest 21: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 21: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from NNPotTest (0 ms total) 21: 21: [----------] 5 tests from NNPotOptionsTest 21: [ RUN ] NNPotOptionsTest.DefaultParameters 21: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] NNPotOptionsTest.OptionSetsActive 21: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 21: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 21: [----------] 5 tests from NNPotOptionsTest (0 ms total) 21: 21: [----------] 5 tests from NNPotTopologyPreprocessorTest 21: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 21: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -84449291 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -3145826 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -537168625 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (8 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -19270665 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (8 ms) 21: [----------] 5 tests from NNPotTopologyPreprocessorTest (23 ms total) 21: 21: [----------] 1 test from NNPotForceProviderTest 21: [ RUN ] NNPotForceProviderTest.CanConstruct 21: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 21: [----------] 1 test from NNPotForceProviderTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 12 tests from 4 test suites ran. (23 ms total) 21: [ PASSED ] 12 tests. 21/90 Test #21: NNPotAppliedForcesUnitTest ................ Passed 0.05 sec test 22 Start 22: AppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 3 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from ElectricFieldTest 22: [ RUN ] ElectricFieldTest.Static 22: [ OK ] ElectricFieldTest.Static (0 ms) 22: [ RUN ] ElectricFieldTest.Oscillating 22: [ OK ] ElectricFieldTest.Oscillating (0 ms) 22: [ RUN ] ElectricFieldTest.Pulsed 22: [ OK ] ElectricFieldTest.Pulsed (0 ms) 22: [----------] 3 tests from ElectricFieldTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 3 tests from 1 test suite ran. (0 ms total) 22: [ PASSED ] 3 tests. 22/90 Test #22: AppliedForcesUnitTest ..................... Passed 0.01 sec test 23 Start 23: ListedForcesTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 132 tests from 9 test suites. 23: [----------] Global test environment set-up. 23: [----------] 24 tests from Bond/ListedForcesTest 23: [ RUN ] Bond/ListedForcesTest.Ifunc/0 23: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/1 23: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/2 23: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/3 23: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/4 23: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/5 23: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/6 23: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/7 23: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/8 23: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/9 23: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/10 23: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/11 23: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/12 23: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/13 23: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/14 23: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/15 23: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/16 23: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/17 23: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/18 23: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/19 23: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/20 23: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/21 23: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/22 23: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/23 23: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 23: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 23: 23: [----------] 33 tests from Angle/ListedForcesTest 23: [ RUN ] Angle/ListedForcesTest.Ifunc/0 23: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/1 23: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/2 23: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/3 23: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/4 23: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/5 23: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/6 23: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/7 23: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/8 23: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/9 23: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/10 23: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/11 23: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/12 23: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/13 23: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/14 23: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/15 23: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/16 23: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/17 23: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/18 23: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/19 23: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/20 23: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/21 23: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/22 23: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/23 23: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/24 23: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/25 23: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/26 23: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/27 23: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/28 23: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/29 23: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/30 23: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/31 23: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/32 23: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 23: [----------] 33 tests from Angle/ListedForcesTest (3 ms total) 23: 23: [----------] 18 tests from Dihedral/ListedForcesTest 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Dihedral/ListedForcesTest (1 ms total) 23: 23: [----------] 12 tests from Polarize/ListedForcesTest 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 23: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 23: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 23: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 23: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 23: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 23: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 23: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 23: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 23: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 23: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 23: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 23: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 23: 23: [----------] 18 tests from Restraints/ListedForcesTest 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 23: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 23: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 23: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 23: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 23: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 23: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 23: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 23: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 23: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 23: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 23: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 23: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 23: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 23: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 23: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 23: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 23: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 23: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Restraints/ListedForcesTest (1 ms total) 23: 23: [----------] 3 tests from BondZeroLength/ListedForcesTest 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 23: 23: [----------] 3 tests from AngleZero/ListedForcesTest 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 23: 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 23: 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 132 tests from 9 test suites ran. (12 ms total) 23: [ PASSED ] 132 tests. 23/90 Test #23: ListedForcesTest .......................... Passed 0.03 sec test 24 Start 24: NbnxmTests 24: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests 24: Test timeout computed to be: 30 24: [==========] Running 383 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 18 tests from KernelSetupTest 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 24: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 24: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 24: [----------] 18 tests from KernelSetupTest (0 ms total) 24: 24: [----------] 2 tests from SimdEnergyAccumulatorTest 24: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 24: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 24: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 24: 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 24: 24: [----------] 360 tests from Combinations/NbnxmKernelTest 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [----------] 360 tests from Combinations/NbnxmKernelTest (391 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 383 tests from 4 test suites ran. (391 ms total) 24: [ PASSED ] 185 tests. 24: [ SKIPPED ] 198 tests, listed below: 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24/90 Test #24: NbnxmTests ................................ Passed 0.41 sec test 25 Start 25: NbnxmGpuTests 25: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 0 tests from 0 test suites. 25: [==========] 0 tests from 0 test suites ran. (0 ms total) 25: [ PASSED ] 0 tests. 25/90 Test #25: NbnxmGpuTests ............................. Passed 0.02 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 26: [----------] 22 tests from ParseCommonArgsTest (2 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (5 ms total) 26: [ PASSED ] 60 tests. 26/90 Test #26: CommandLineUnitTests ...................... Passed 0.02 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/90 Test #27: DomDecTests ............................... Passed 0.01 sec test 28 Start 28: DomDecMpiTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (18 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (13 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (38 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (22 ms) 28: [----------] 4 tests from HaloExchangeTest (94 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (94 ms total) 28: [ PASSED ] 4 tests. 28/90 Test #28: DomDecMpiTests ............................ Passed 0.11 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (62 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (6 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (147 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (9 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (6 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (9 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (10 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (38 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (227 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/90 Test #29: EwaldUnitTests ............................ Passed 0.26 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (2 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (3 ms) 30: [----------] 2 tests from ManyFFTTest (6 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (0 ms) 30: [----------] 1 test from FFTTest (1 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (6 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (15 ms total) 30: [ PASSED ] 15 tests. 30/90 Test #30: FFTUnitTests .............................. Passed 0.04 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 67 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 67 tests from 22 test suites ran. (0 ms total) 31: [ PASSED ] 67 tests. 31/90 Test #31: GpuUtilsUnitTests ......................... Passed 0.02 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 22 tests from 10 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (0 ms) 32: [----------] 1 test from CpuInfoTest (0 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (8 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (7 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (7 ms) 32: [----------] 4 tests from HardwareTopologyTest (34 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 1 test from UuidStringTest 32: [ RUN ] UuidStringTest.Works 32: [ OK ] UuidStringTest.Works (0 ms) 32: [----------] 1 test from UuidStringTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (2 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 22 tests from 10 test suites ran. (47 ms total) 32: [ PASSED ] 22 tests. 32: 32: YOU HAVE 1 DISABLED TEST 32: 32/90 Test #32: HardwareUnitTests ......................... Passed 0.06 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 328 tests from 41 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 8 tests from ComplexNumberTest 33: [ RUN ] ComplexNumberTest.RealComplexMultiply 33: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.RealComplexExp 33: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAdd 33: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexSubtract 33: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexMultiply 33: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexDivision 33: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexConjugate 33: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAbs2 33: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 33: [----------] 8 tests from ComplexNumberTest (0 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (1 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (12 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (12 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (27 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (1 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 22 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.canAddMatrix 33: [ OK ] MatrixTest.canAddMatrix (0 ms) 33: [ RUN ] MatrixTest.canSubstractMatrix 33: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 33: [ RUN ] MatrixTest.canNegateMatrix 33: [ OK ] MatrixTest.canNegateMatrix (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 33: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixMultiplication 33: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 22 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 41 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.UsableInConstexpr 33: [ OK ] RVecTest.UsableInConstexpr (0 ms) 33: [----------] 41 tests from RVecTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 328 tests from 41 test suites ran. (31 ms total) 33: [ PASSED ] 328 tests. 33/90 Test #33: MathUnitTests ............................. Passed 0.05 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (4 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (4 ms total) 34: [ PASSED ] 21 tests. 34/90 Test #34: MdrunUtilityUnitTests ..................... Passed 0.02 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (46 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (55 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (44 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (31 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (47 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (55 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (282 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (51 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (31 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (36 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (51 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (51 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (63 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (43 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (331 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (614 ms total) 35: [ PASSED ] 13 tests. 35/90 Test #35: MdrunUtilityMpiUnitTests .................. Passed 0.63 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/90 Test #36: MDSpanTests ............................... Passed 0.01 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 37: [----------] 2 tests from CheckpointDataTest (3 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (0 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (4 ms total) 37: [ PASSED ] 97 tests. 37/90 Test #37: MdtypesUnitTest ........................... Passed 0.02 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (0 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (1 ms total) 38: [ PASSED ] 22 tests. 38/90 Test #38: OnlineHelpUnitTests ....................... Passed 0.02 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 112 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 16 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 39: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 39: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (0 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 112 tests from 18 test suites ran. (2 ms total) 39: [ PASSED ] 112 tests. 39/90 Test #39: OptionsUnitTests .......................... Passed 0.02 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (0 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (3 ms total) 40: [ PASSED ] 37 tests. 40/90 Test #40: PbcutilUnitTest ........................... Passed 0.02 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (1 ms total) 41: [ PASSED ] 44 tests. 41/90 Test #41: RandomUnitTests ........................... Passed 0.02 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/90 Test #42: RestraintTests ............................ Passed 0.01 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (0 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (6 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (14 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (2 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (10 ms) 43: [----------] 10 tests from SplineTableTest/0 (46 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (0 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (13 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (27 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (28 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (5 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (22 ms) 43: [----------] 10 tests from SplineTableTest/1 (98 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (145 ms total) 43: [ PASSED ] 20 tests. 43/90 Test #43: TableUnitTests ............................ Passed 0.16 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (0 ms total) 44: [ PASSED ] 3 tests. 44/90 Test #44: TaskAssignmentUnitTests ................... Passed 0.02 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (5 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (6 ms total) 45: [ PASSED ] 6 tests. 45/90 Test #45: GmxTimingTests ............................ Passed 0.02 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (1 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 46: [----------] 3 tests from IndexTest (5 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (1 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (5 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (12 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/90 Test #46: TopologyTest .............................. Passed 0.04 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (0 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 47: [----------] 10 tests from PullTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (0 ms total) 47: [ PASSED ] 10 tests. 47/90 Test #47: PullTest .................................. Passed 0.01 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 247 tests from 19 test suites. 48: [----------] Global test environment set-up. 48: [----------] 6 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [----------] 6 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (0 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 13 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsDouble 48: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (1 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (0 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (0 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (0 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (1 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (0 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (0 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (0 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (0 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (0 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (0 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (0 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (0 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (0 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (0 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (24 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 247 tests from 19 test suites ran. (25 ms total) 48: [ PASSED ] 247 tests. 48/90 Test #48: SimdUnitTests ............................. Passed 0.04 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/90 Test #49: CompatibilityHelpersTests ................. Passed 0.01 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (0 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (443 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (217 ms) 50: [----------] 2 tests from GmxChiTest (730 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (5 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (0 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (0 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (0 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (0 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (0 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (0 ms) 50: [----------] 10 tests from MindistTest (9 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (10 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (751 ms total) 50: [ PASSED ] 31 tests. 50/90 Test #50: GmxAnaTest ................................ Passed 0.77 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 212 tests from 15 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ConvertInteractionsTest 51: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 51: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 51: [----------] 1 test from ConvertInteractionsTest (0 ms total) 51: 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 51: [----------] 4 tests from GenconfTest (2 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to -419479809 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (267 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to -35520609 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (254 ms) 51: [----------] 2 tests from GenionTest (521 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 51: [----------] 1 test from GenRestrTest (1 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 51: 51: [----------] 3 tests from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Setting the LD random seed to 1990152187 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1006577273 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 51: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 51: coefficients that do not sum to zero. This does not affect the simulation 51: and can be ignored, unless you are comparing potential energy values with 51: other force field ports and/or MD software. 51: First such dihedral in molecule A, involving atoms 0 2 1 3 51: 51: 51: NOTE 2 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 3 NOTEs 51: Setting the LD random seed to -1075876418 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -27267989 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 51: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 51: Setting the LD random seed to -539263053 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -2229153 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (6 ms) 51: [----------] 3 tests from GromppDirectiveTest (12 ms total) 51: 51: [----------] 6 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (3 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (0 ms) 51: [----------] 6 tests from InsertMoleculesTest (7 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartitioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (0 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (5 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (4 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (5 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (5 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (8 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (2 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (82 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (2 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (11 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (11 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (7 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (53 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 51: [----------] 6 tests from SolvateTest (90 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (0 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (4 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (1 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (18 ms total) 51: 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 51: Setting the LD random seed to -310771986 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (7 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 51: Setting the LD random seed to 2147483499 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (11 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to 2042099567 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -54542849 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 51: Setting the LD random seed to 233823993 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (13 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 51: Setting the LD random seed to -1130629171 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1145242625 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (12 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 51: Setting the LD random seed to -541066273 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (13 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 51: Setting the LD random seed to 1846437341 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -293651265 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (14 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 51: Setting the LD random seed to -776085571 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -147358214 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (12 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 51: Setting the LD random seed to -1412968457 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -672172705 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (16 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 51: Setting the LD random seed to -75503235 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1122714799 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (19 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 51: Setting the LD random seed to -549720713 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -673321479 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (12 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 51: Setting the LD random seed to 2076176123 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -17318060 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (15 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 51: Setting the LD random seed to -541336069 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -547504673 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (12 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to 2145973803 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -72454913 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -1083248693 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1610793329 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (2 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 51: Setting the LD random seed to -8914049 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 51: Setting the LD random seed to -353417 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 2013265916 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 51: Setting the LD random seed to 2045243386 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (5 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -2 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -40939150 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (3 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 51: Setting the LD random seed to -1211572420 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (5 ms) 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (197 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 212 tests from 15 test suites ran. (935 ms total) 51: [ PASSED ] 172 tests. 51: [ SKIPPED ] 40 tests, listed below: 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51/90 Test #51: GmxPreprocessTests ........................ Passed 0.95 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (55 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (58 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (852 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (852 ms total) 52: [ PASSED ] 30 tests. 52/90 Test #52: Pdb2gmx1Test .............................. Passed 0.87 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (46 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (536 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (48 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (25 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (564 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (1100 ms total) 53: [ PASSED ] 40 tests. 53/90 Test #53: Pdb2gmx2Test .............................. Passed 1.12 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (58 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (28 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (330 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (60 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (66 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (326 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (20 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (17 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (156 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (52 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.563 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (190 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (48 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.563 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (299 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (51 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (589 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (1465 ms total) 54: [ PASSED ] 39 tests. 54/90 Test #54: Pdb2gmx3Test .............................. Passed 1.48 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (41 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (39 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (37 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (39 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (0 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (75 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (20 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (44 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (1 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (34 ms) 55: [----------] 10 tests from AutocorrTest (337 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (5 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (0 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (1 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (3 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (10 ms) 55: [----------] 10 tests from ExpfitTest (26 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (366 ms total) 55: [ PASSED ] 21 tests. 55/90 Test #55: CorrelationsTest .......................... Passed 0.38 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (5 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (2 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (0 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from LifetimeModuleTest (1 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (18 ms total) 56: [ PASSED ] 69 tests. 56/90 Test #56: AnalysisDataUnitTests ..................... Passed 0.03 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (6 ms) 57: [----------] 1 test from OutputSelectorDeathTest (6 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (4 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (0 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 57: [----------] 5 tests from SetAtomsTest (4 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (4 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (7 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (40 ms total) 57: [ PASSED ] 67 tests. 57/90 Test #57: CoordinateIOTests ......................... Passed 0.06 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 393 tests from 21 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 58: [----------] 11 tests from AngleModuleTest (17 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (0 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (0 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) 58: [----------] 5 tests from ClustsizeTest (4 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (5 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (2 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (13 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (6 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (5 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (4 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (10 ms) 58: [----------] 6 tests from DistanceModuleTest (31 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (8 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (9 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (43 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (44 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (88 ms total) 58: 58: [----------] 13 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -4464898 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (14 ms) 58: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.100 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 58: Analyzed 21 frames, last time 2.000 58: Setting the LD random seed to -686827093 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (15 ms) 58: [ RUN ] MsdModuleTest.trestartLessThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1153450017 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartLessThanDt (11 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1559196636 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (18 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -270556482 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (12 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -21364875 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (13 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -131075079 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (13 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -323490090 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (13 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -1097833 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (14 ms) 58: [----------] 13 tests from MsdModuleTest (134 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 58: [----------] 9 tests from PairDistanceModuleTest (11 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (10 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (9 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (4 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 58: [----------] 5 tests from RdfModuleTest (47 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (6 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (4 ms) 58: [----------] 5 tests from SasaModuleTest (22 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (2 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 58: [----------] 8 tests from SelectModuleTest (12 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (4 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 58: [----------] 10 tests from SurfaceAreaTest (8 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Setting the LD random seed to -1477968932 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (271 ms) 58: [----------] 4 tests from TopologyInformation (273 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 58: [----------] 4 tests from TrajectoryModuleTest (5 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 192 tests from MoleculeTests/DsspModuleTest 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 58: [----------] 192 tests from MoleculeTests/DsspModuleTest (2072 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (12 ms total) 58: 58: [----------] 96 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (9 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/6 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/6 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/7 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/7 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/8 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/8 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/9 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/9 (9 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/10 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/10 (11 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/11 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/11 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/12 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/12 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/13 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/13 (9 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/14 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/14 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/15 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/15 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/16 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/16 (12 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/17 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/17 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/18 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/18 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/19 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/19 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/20 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/20 (9 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/21 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/21 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/22 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/22 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/23 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/23 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/24 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/24 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/25 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/25 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/26 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/26 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/27 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/27 (7 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/28 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/28 (13 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/29 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/29 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/30 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/30 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/31 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/31 (8 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/32 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/32 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/33 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/33 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/34 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/34 (56 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/35 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/35 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/36 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/36 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/37 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/37 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/38 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/38 (54 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/39 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/39 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/40 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/40 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/41 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/41 (55 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/42 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/42 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/43 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/43 (53 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/44 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/44 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/45 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/45 (54 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/46 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/46 (51 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/47 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/47 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/48 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/48 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/49 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/49 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/50 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/50 (53 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/51 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/51 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/52 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/52 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/53 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/53 (41 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/54 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/54 (58 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/55 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/55 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/56 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/56 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/57 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/57 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/58 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/58 (42 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/59 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/59 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/60 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/60 (62 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/61 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/61 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/62 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/62 (60 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/63 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/63 (54 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/64 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/64 (54 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/65 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/65 (51 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/66 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/66 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/67 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/67 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/68 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/68 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/69 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/69 (50 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/70 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/70 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/71 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/71 (55 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/72 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/72 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/73 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/73 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/74 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/74 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/75 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/75 (55 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/76 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/76 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/77 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/77 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/78 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/78 (51 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/79 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/79 (46 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/80 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/80 (56 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/81 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/81 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/82 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/82 (61 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/83 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/83 (57 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/84 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/84 (43 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/85 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/85 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/86 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/86 (44 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/87 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/87 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/88 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/88 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/89 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/89 (47 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/90 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/90 (52 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/91 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/91 (48 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/92 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/92 (53 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/93 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/93 (49 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/94 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/94 (45 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/95 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/95 (48 ms) 58: [----------] 96 tests from HBondTests/HbondModuleTest (3841 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (166 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (6 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (39 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (219 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 393 tests from 21 test suites ran. (6832 ms total) 58: [ PASSED ] 393 tests. 58/90 Test #58: TrajectoryAnalysisUnitTests ............... Passed 6.86 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 12 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 137 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (5 ms) 59: [----------] 1 test from DhdlTest (6 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 137 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (8 ms) 59: [----------] 1 test from OriresTest (8 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 59: [----------] 5 tests from EnergyTest (4 ms total) 59: 59: [----------] 3 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (107 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (59 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (33 ms) 59: [----------] 3 tests from ViscosityTest (200 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 12 tests from 5 test suites ran. (220 ms total) 59: [ PASSED ] 12 tests. 59/90 Test #59: EnergyAnalysisUnitTests ................... Passed 0.23 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 63 tests from 8 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to 2147477481 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = 2147477481 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com: not available 60: posres-comB: not available 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: nnpot: 60: active = false 60: modelfile = model.pt 60: input-group = System 60: model-input1 = 60: model-input2 = 60: model-input3 = 60: model-input4 = 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 57082 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 60: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 60: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 60: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 60: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 60: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 60: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 60: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 60: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 60: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 60: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 60: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 60: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 60: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 60: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 60: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 60: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 60: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 60: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 60: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 60: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 60: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 60: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 60: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 60: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 60: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 60: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 60: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 60: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 60: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 60: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 60: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 60: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 60: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 60: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 60: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 60: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 60: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 60: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 60: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 60: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 60: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 60: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 60: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 60: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 60: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 60: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 60: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 60: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 60: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 60: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 60: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 60: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 60: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 60: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 60: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 60: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 60: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 60: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 60: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 60: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 60: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 60: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 60: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 60: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 60: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 60: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 60: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 60: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 60: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 60: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 60: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 60: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 60: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 60: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 60: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 60: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 60: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 60: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 60: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 60: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 60: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 60: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 60: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 60: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 60: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 60: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 60: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 60: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 60: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 60: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 60: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 60: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 60: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 60: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 60: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 60: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 60: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 60: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 60: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 60: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 60: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 60: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 60: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 60: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 60: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 60: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 60: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 60: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 60: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 60: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 60: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 60: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 60: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 60: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 60: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 60: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 60: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 60: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 60: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 60: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 60: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 60: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 60: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 60: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 60: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 60: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 60: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 60: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 60: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 60: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 60: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 60: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 60: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 60: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: NN Potential: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (4 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 60: [----------] 2 tests from DumpTest (5 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (0 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (1 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (0 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (0 ms) 60: [----------] 7 tests from GmxMakeNdx (4 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to 2145713903 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (0 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -590913537 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (270 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -424058979 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (259 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -289542659 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (264 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -671096834 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (280 ms) 60: [----------] 4 tests from ConvertTprTest (1075 ms total) 60: 60: [----------] 1 test from ConvertTprNoVelocityTest 60: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: 60: NOTE 3 [file lysozyme.top, line 1465]: 60: Zero-step energy minimization will alter the coordinates before 60: calculating the energy. If you just want the energy of a single point, 60: try zero-step MD (with unconstrained_start = yes). To do multiple 60: single-point energy evaluations of different configurations of the same 60: topology, use mdrun -rerun. 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -81019809 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (275 ms) 60: [----------] 1 test from ConvertTprNoVelocityTest (275 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (4 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (8 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 63 tests from 8 test suites ran. (1912 ms total) 60: [ PASSED ] 63 tests. 60/90 Test #60: ToolUnitTests ............................. Passed 1.93 sec test 61 Start 61: ToolWithLeaksUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests 61: Test timeout computed to be: 1920 61: [==========] Running 2 tests from 2 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from ConvertTprTest 61: [ RUN ] ConvertTprTest.selectIndexTest 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Setting the LD random seed to -1611170833 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprTest.selectIndexTest (281 ms) 61: [----------] 1 test from ConvertTprTest (281 ms total) 61: 61: [----------] 1 test from ConvertTprNoVelocityTest 61: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: 61: NOTE 3 [file lysozyme.top, line 1465]: 61: Zero-step energy minimization will alter the coordinates before 61: calculating the energy. If you just want the energy of a single point, 61: try zero-step MD (with unconstrained_start = yes). To do multiple 61: single-point energy evaluations of different configurations of the same 61: topology, use mdrun -rerun. 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Setting the LD random seed to 2146395775 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (266 ms) 61: [----------] 1 test from ConvertTprNoVelocityTest (266 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 2 tests from 2 test suites ran. (547 ms total) 61: [ PASSED ] 2 tests. 61/90 Test #61: ToolWithLeaksUnitTests .................... Passed 0.56 sec test 62 Start 62: FileIOTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/FileIOTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests 62: Test timeout computed to be: 30 62: [==========] Running 421 tests from 17 test suites. 62: [----------] Global test environment set-up. 62: [----------] 4 tests from Checkpoint 62: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 62: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 62: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 62: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripInt64 62: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripReal 62: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 62: [----------] 4 tests from Checkpoint (0 ms total) 62: 62: [----------] 1 test from StructureIOTest 62: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 62: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 62: [----------] 1 test from StructureIOTest (0 ms total) 62: 62: [----------] 2 tests from FileMD5Test 62: [ RUN ] FileMD5Test.CanComputeMD5 62: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 62: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 62: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 62: [----------] 2 tests from FileMD5Test (0 ms total) 62: 62: [----------] 4 tests from FileTypeTest 62: [ RUN ] FileTypeTest.CorrectValueForEmptyString 62: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForNoExtension 62: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 62: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 62: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 62: [----------] 4 tests from FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from ColorMapTest 62: [ RUN ] ColorMapTest.CanReadFromFile 62: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 62: [ RUN ] ColorMapTest.CanWriteToFile 62: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 62: [ RUN ] ColorMapTest.RoundTrip 62: [ OK ] ColorMapTest.RoundTrip (0 ms) 62: [ RUN ] ColorMapTest.SearchWorks 62: [ OK ] ColorMapTest.SearchWorks (0 ms) 62: [----------] 4 tests from ColorMapTest (0 ms total) 62: 62: [----------] 4 tests from MatioTest 62: [ RUN ] MatioTest.CanWriteToFile 62: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 62: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanConvertToNewRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 62: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (2 ms) 62: [----------] 4 tests from MatioTest (2 ms total) 62: 62: [----------] 3 tests from MrcSerializer 62: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 62: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 62: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 62: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 62: [----------] 3 tests from MrcSerializer (0 ms total) 62: 62: [----------] 4 tests from MrcDensityMap 62: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 62: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 62: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 62: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 62: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 62: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 62: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 62: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 62: [----------] 4 tests from MrcDensityMap (0 ms total) 62: 62: [----------] 8 tests from MrcDensityMapHeaderTest 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 62: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.IsSane 62: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 62: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 62: 62: [----------] 10 tests from ReadTest 62: [ RUN ] ReadTest.get_eint_ReadsInteger 62: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_eint64_ReadsInteger 62: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsInteger 62: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsFloat 62: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 62: [ RUN ] ReadTest.get_ereal_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not a 62: real value 62: 62: 62: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 62: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 62: [----------] 10 tests from ReadTest (0 ms total) 62: 62: [----------] 3 tests from TimeControlTest 62: [ RUN ] TimeControlTest.UnSetHasNoValue 62: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 62: [ RUN ] TimeControlTest.CanSetValue 62: [ OK ] TimeControlTest.CanSetValue (0 ms) 62: [ RUN ] TimeControlTest.CanUnsetValueAgain 62: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 62: [----------] 3 tests from TimeControlTest (0 ms total) 62: 62: [----------] 1 test from FileIOXdrSerializerTest 62: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 62: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 62: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 62: 62: [----------] 1 test from TngTest 62: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 62: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 62: [----------] 1 test from TngTest (0 ms total) 62: 62: [----------] 4 tests from XvgioTest 62: [ RUN ] XvgioTest.readXvgIntWorks 62: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgRealWorks 62: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 62: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgDeprecatedWorks 62: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 62: [----------] 4 tests from XvgioTest (0 ms total) 62: 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 62: 62: [----------] 360 tests from FileTypeMatch/FileTypeTest 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 62: [----------] 360 tests from FileTypeMatch/FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 421 tests from 17 test suites ran. (7 ms total) 62: [ PASSED ] 421 tests. 62/90 Test #62: FileIOTests ............................... Passed 0.03 sec test 63 Start 63: SelectionUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests 63: Test timeout computed to be: 30 63: [==========] Running 201 tests from 11 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from IndexGroupTest 63: [ RUN ] IndexGroupTest.RemovesDuplicates 63: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 63: [----------] 1 test from IndexGroupTest (0 ms total) 63: 63: [----------] 15 tests from IndexBlockTest 63: [ RUN ] IndexBlockTest.CreatesUnknownBlock 63: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesAtomBlock 63: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesSingleBlock 63: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 63: [----------] 15 tests from IndexBlockTest (1 ms total) 63: 63: [----------] 11 tests from IndexMapTest 63: [ RUN ] IndexMapTest.InitializesAtomBlock 63: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 63: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 63: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 63: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 63: [ RUN ] IndexMapTest.InitializesMoleculeBlock 63: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsSingleBlock 63: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocks 63: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 63: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 63: [ RUN ] IndexMapTest.HandlesMultipleRequests 63: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 63: [----------] 11 tests from IndexMapTest (1 ms total) 63: 63: [----------] 3 tests from IndexGroupsAndNamesTest 63: [ RUN ] IndexGroupsAndNamesTest.containsNames 63: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 63: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 63: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 63: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 63: 63: [----------] 15 tests from NeighborhoodSearchTest 63: [ RUN ] NeighborhoodSearchTest.SimpleSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 63: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (9 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchBox 63: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 63: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 63: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 63: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 63: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (23 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 63: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 63: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 63: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 63: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 63: [----------] 15 tests from NeighborhoodSearchTest (55 ms total) 63: 63: [----------] 13 tests from PositionCalculationTest 63: [ RUN ] PositionCalculationTest.ComputesAtomPositions 63: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 63: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionMask 63: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 63: [----------] 13 tests from PositionCalculationTest (1 ms total) 63: 63: [----------] 33 tests from SelectionCollectionTest 63: [ RUN ] SelectionCollectionTest.HandlesNoSelections 63: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 63: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 63: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 63: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 63: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 63: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 63: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 63: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 63: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 63: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 63: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 63: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 63: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 63: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 63: [----------] 33 tests from SelectionCollectionTest (7 ms total) 63: 63: [----------] 14 tests from SelectionCollectionInteractiveTest 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 63: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 63: [----------] 14 tests from SelectionCollectionInteractiveTest (3 ms total) 63: 63: [----------] 70 tests from SelectionCollectionDataTest 63: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 63: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 63: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResnr 63: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 63: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 63: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 63: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesChain 63: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMass 63: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCharge 63: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 63: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 63: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 63: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBeta 63: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResname 63: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 63: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 63: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 63: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 63: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 63: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 63: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 63: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 63: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 63: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 63: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (6 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 63: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 63: [----------] 70 tests from SelectionCollectionDataTest (41 ms total) 63: 63: [----------] 17 tests from SelectionOptionTest 63: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 63: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 63: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 63: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 63: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptySelections 63: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 63: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelections 63: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 63: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesAdjuster 63: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 63: [----------] 17 tests from SelectionOptionTest (3 ms total) 63: 63: [----------] 9 tests from SelectionFileOptionTest 63: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 63: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 63: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 63: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 201 tests from 11 test suites ran. (116 ms total) 63: [ PASSED ] 201 tests. 63/90 Test #63: SelectionUnitTests ........................ Passed 0.13 sec test 64 Start 64: MdrunOutputTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 12 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from MdrunTest 64: [ RUN ] MdrunTest.WritesHelp 64: [ OK ] MdrunTest.WritesHelp (9 ms) 64: [----------] 1 test from MdrunTest (9 ms total) 64: 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -25175567 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 196.5 64: (ns/day) (hour/ns) 64: Performance: 46.926 0.511 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (11 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -1141421576 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 186.8 64: (ns/day) (hour/ns) 64: Performance: 343.333 0.070 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (4 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -823137003 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 186.9 64: (ns/day) (hour/ns) 64: Performance: 322.553 0.074 64: Reading frame 0 time 0.000 64: # Atoms 3 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (7 ms) 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (24 ms total) 64: 64: [----------] 2 tests from Argon12/OutputFiles 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 191.3 64: (ns/day) (hour/ns) 64: Performance: 2072.878 0.012 64: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (4 ms) 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 195.4 64: (ns/day) (hour/ns) 64: Performance: 1337.515 0.018 64: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (11 ms) 64: [----------] 2 tests from Argon12/OutputFiles (16 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/Trajectories 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -1216621909 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 196.6 64: (ns/day) (hour/ns) 64: Performance: 240.333 0.100 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (10 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -8197 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.4 64: (ns/day) (hour/ns) 64: Performance: 322.450 0.074 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (11 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -30141 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 433.997 0.055 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (11 ms) 64: [----------] 3 tests from MdrunCanWrite/Trajectories (32 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -807406594 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 190.2 64: (ns/day) (hour/ns) 64: Performance: 344.803 0.070 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (6 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: The Berendsen barostat does not generate any strictly correct ensemble, 64: and should not be used for new production simulations (in our opinion). 64: We recommend using the C-rescale barostat instead. 64: 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to 2126479350 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.037 0.019 199.5 64: (ns/day) (hour/ns) 64: Performance: 13.825 1.736 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (30 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1627438209 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.035 0.017 199.4 64: (ns/day) (hour/ns) 64: Performance: 14.971 1.603 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (26 ms) 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories (63 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 12 tests from 5 test suites ran. (177 ms total) 64: [ PASSED ] 12 tests. 64/90 Test #64: MdrunOutputTests .......................... Passed 0.19 sec test 65 Start 65: MdrunModulesTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 15 tests from 3 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from DensityFittingTest 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.85652608067156e+03 65: Maximum force = 4.50998690851897e+03 on atom 3 65: Norm of force = 1.68168494163492e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -571091570 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (19 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -9.82077921283928e+03 65: Maximum force = 7.39548334240075e+03 on atom 2 65: Norm of force = 2.78250777177324e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -145015172 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (17 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (5 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Overriding nsteps with value passed on the command line: 4 steps 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 4 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 5 steps. 65: Potential Energy = -1.09549987768583e+04 65: Maximum force = 7.47247842297763e+03 on atom 2 65: Norm of force = 2.77579925913607e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1369718786 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (9 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (10 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.85652608067156e+03 65: Maximum force = 4.50998690851897e+03 on atom 3 65: Norm of force = 1.68168494163492e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -319333639 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (8 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -2.71386626041483e+04 65: Maximum force = 6.78276506555709e+03 on atom 2 65: Norm of force = 1.96088641457984e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1879043823 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (8 ms) 65: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: Setting the LD random seed to 1264348934 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (7 ms) 65: [ RUN ] DensityFittingTest.CheckpointWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (2) 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -537379012 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.007 0.004 196.9 65: (ns/day) (hour/ns) 65: Performance: 68.272 0.352 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.002 0.001 191.2 65: (ns/day) (hour/ns) 65: Performance: 415.487 0.058 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (16 ms) 65: [----------] 9 tests from DensityFittingTest (103 ms total) 65: 65: [----------] 4 tests from MimicTest 65: [ RUN ] MimicTest.OneQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.008 0.004 198.6 65: (ns/day) (hour/ns) 65: Performance: 20.916 1.147 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -165059 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.OneQuantumMol (15 ms) 65: [ RUN ] MimicTest.AllQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 21 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 181.6 65: (ns/day) (hour/ns) 65: Performance: 444.103 0.054 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 525319580 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.AllQuantumMol (8 ms) 65: [ RUN ] MimicTest.TwoQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 60 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.010 0.005 198.8 65: (ns/day) (hour/ns) 65: Performance: 17.813 1.347 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1878981486 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.TwoQuantumMol (10 ms) 65: [ RUN ] MimicTest.BondCuts 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 66.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: NVE simulation: will use the initial temperature of 300.368 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 53 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.012 0.006 199.2 65: (ns/day) (hour/ns) 65: Performance: 14.145 1.697 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1086596551 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.BondCuts (20 ms) 65: [----------] 4 tests from MimicTest (54 ms total) 65: 65: [----------] 2 tests from WithIntegrator/ImdTest 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 65: Generating 1-4 interactions: fudge = 1 65: 65: NOTE 1 [file glycine_vacuo.top, line 12]: 65: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 65: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 65: the time step of 2.0e-03 ps. 65: Maybe you forgot to change the constraints mdp option. 65: 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 37873. 65: IMD: -imdwait not set, starting simulation. 65: starting mdrun 'Glycine' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -67650050 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 18 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.033 0.016 199.4 65: (ns/day) (hour/ns) 65: Performance: 31.507 0.762 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (81 ms) 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 65: apply to steep. 65: 65: Generating 1-4 interactions: fudge = 1 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 34921. 65: IMD: -imdwait not set, starting simulation. 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = 1.19770464690297e+03 65: Maximum force = 1.77948604657896e+04 on atom 9 65: Norm of force = 7.87328617833980e+03 65: Setting the LD random seed to 796891131 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (81 ms) 65: [----------] 2 tests from WithIntegrator/ImdTest (163 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 15 tests from 3 test suites ran. (348 ms total) 65: [ PASSED ] 15 tests. 65/90 Test #65: MdrunModulesTests ......................... Passed 0.36 sec test 66 Start 66: MdrunIOTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 76 tests from 13 test suites. 66: [----------] Global test environment set-up. 66: [----------] 9 tests from GromppTest 66: [ RUN ] GromppTest.EmptyMdpFileWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -102843417 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.EmptyMdpFileWorks (2 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group rest: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to 1365041145 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group Methanol: Single, 3 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 3.0 280.0 66: 6.0- 270.0 66: Simulated annealing for group SOL: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group Methanol is 7.20 66: Number of degrees of freedom in T-Coupling group SOL is 4.80 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -30539939 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 66: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 66: Setting the LD random seed to 1534028799 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (8 ms) 66: [ RUN ] GromppTest.HandlesMaxwarn 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: The Berendsen thermostat does not generate the correct kinetic energy 66: distribution, and should not be used for new production simulations (in 66: our opinion). We would recommend the V-rescale thermostat. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: There was 1 WARNING 66: Setting the LD random seed to -1610844551 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.HandlesMaxwarn (3 ms) 66: [ RUN ] GromppTest.MaxwarnShouldBePositive 66: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 66: [ RUN ] GromppTest.ValidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -1349142529 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 66: [ RUN ] GromppTest.InvalidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 Setting the LD random seed to -8716321 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: [ OK ] GromppTest.InvalidTransformationCoord (2 ms) 66: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 66: Setting the LD random seed to 1869475974 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (5 ms) 66: [----------] 9 tests from GromppTest (32 ms total) 66: 66: [----------] 6 tests from MdrunTerminationTest 66: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -538066947 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 195.2 66: (ns/day) (hour/ns) 66: Performance: 169.340 0.142 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.2 66: (ns/day) (hour/ns) 66: Performance: 337.838 0.071 66: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (12 ms) 66: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 1, rlist from 1.035 to 1 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 100 steps, 0.1 ps. 66: 66: Step 14: Run time exceeded 0.000 hours, will terminate the run within 200 steps 66: Setting the LD random seed to 2003741695 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.014 0.007 198.3 66: (ns/day) (hour/ns) 66: Performance: 1218.050 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 102 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 100 66: Runtime for the run 0.1 ps 66: Run end step 100 66: Run end time 0.1 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 102 66: Runtime for the run 0.102 ps 66: Run end step 102 66: Run end time 0.102 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.7 66: (ns/day) (hour/ns) 66: Performance: 498.699 0.048 66: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (13 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 1809711096 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 188.0 66: (ns/day) (hour/ns) 66: Performance: 523.934 0.046 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 192.4 66: (ns/day) (hour/ns) 66: Performance: 545.217 0.044 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 6 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 192.9 66: (ns/day) (hour/ns) 66: Performance: 340.804 0.070 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 8 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 8 66: Runtime for the run 0.008 ps 66: Run end step 8 66: Run end time 0.008 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.9 66: (ns/day) (hour/ns) 66: Performance: 508.972 0.047 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: NOTE: 26 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 170.3 66: (ns/day) (hour/ns) 66: Performance: 656.500 0.037 66: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (19 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -542244873 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 187.5 66: (ns/day) (hour/ns) 66: Performance: 563.005 0.043 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.8 66: (ns/day) (hour/ns) 66: Performance: 511.992 0.047 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (11 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1594490893 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 187.6 66: (ns/day) (hour/ns) 66: Performance: 548.518 0.044 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (5 ms) 66: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -134228037 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 186.1 66: (ns/day) (hour/ns) 66: Performance: 527.237 0.046 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 191.6 66: (ns/day) (hour/ns) 66: Performance: 556.949 0.043 66: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (8 ms) 66: [----------] 6 tests from MdrunTerminationTest (70 ms total) 66: 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.137 0.069 199.8 66: (ns/day) (hour/ns) 66: Performance: 21.402 1.121 66: trr version: GMX_trn_file (double precision) 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (76 ms) 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.169 0.085 199.9 66: (ns/day) (hour/ns) 66: Performance: 17.324 1.385 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (91 ms) 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (168 ms total) 66: 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.122 0.061 199.9 66: (ns/day) (hour/ns) 66: Performance: 24.048 0.998 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.791 1.053 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.757 1.055 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (146 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.121 0.061 199.8 66: (ns/day) (hour/ns) 66: Performance: 24.162 0.993 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.925 1.047 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.771 1.054 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (145 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.138 0.069 199.9 66: (ns/day) (hour/ns) 66: Performance: 21.284 1.128 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.864 1.208 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.415 1.176 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (161 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.147 0.073 199.9 66: (ns/day) (hour/ns) 66: Performance: 20.042 1.197 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.819 1.211 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.509 1.170 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (166 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.5 66: (ns/day) (hour/ns) 66: Performance: 64.196 0.374 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.0 66: (ns/day) (hour/ns) 66: Performance: 1248.657 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.1 66: (ns/day) (hour/ns) 66: Performance: 1186.428 0.020 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (36 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.012 0.006 198.0 66: (ns/day) (hour/ns) 66: Performance: 252.805 0.095 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.7 66: (ns/day) (hour/ns) 66: Performance: 1277.513 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.8 66: (ns/day) (hour/ns) 66: Performance: 908.240 0.026 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (17 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.9 66: (ns/day) (hour/ns) 66: Performance: 1591.062 0.015 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.9 66: (ns/day) (hour/ns) 66: Performance: 1173.620 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.009 0.004 197.5 66: (ns/day) (hour/ns) 66: Performance: 174.095 0.138 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (15 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.114 0.057 199.8 66: (ns/day) (hour/ns) 66: Performance: 25.713 0.933 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.008 0.004 197.2 66: (ns/day) (hour/ns) 66: Performance: 187.755 0.128 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.3 66: (ns/day) (hour/ns) 66: Performance: 1122.330 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (78 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.5 66: (ns/day) (hour/ns) 66: Performance: 1854.483 0.013 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 191.8 66: (ns/day) (hour/ns) 66: Performance: 564.760 0.042 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.2 66: (ns/day) (hour/ns) 66: Performance: 1178.284 0.020 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (15 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.008 0.004 196.8 66: (ns/day) (hour/ns) 66: Performance: 355.919 0.067 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.2 66: (ns/day) (hour/ns) 66: Performance: 1189.023 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.8 66: (ns/day) (hour/ns) 66: Performance: 1201.286 0.020 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (24 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.2 66: (ns/day) (hour/ns) 66: Performance: 1364.170 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.2 66: (ns/day) (hour/ns) 66: Performance: 874.863 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.014 0.007 198.4 66: (ns/day) (hour/ns) 66: Performance: 112.648 0.213 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (21 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 22 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 195.1 66: (ns/day) (hour/ns) 66: Performance: 1195.767 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.1 66: (ns/day) (hour/ns) 66: Performance: 958.135 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 191.1 66: (ns/day) (hour/ns) 66: Performance: 882.199 0.027 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (12 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.5 66: (ns/day) (hour/ns) 66: Performance: 195.011 0.123 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.5 66: (ns/day) (hour/ns) 66: Performance: 1220.618 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.3 66: (ns/day) (hour/ns) 66: Performance: 808.500 0.030 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (19 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.2 66: (ns/day) (hour/ns) 66: Performance: 2017.882 0.012 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.073 0.036 199.7 66: (ns/day) (hour/ns) 66: Performance: 21.318 1.126 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.072 0.036 199.7 66: (ns/day) (hour/ns) 66: Performance: 21.429 1.120 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (93 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.169 0.085 199.9 66: (ns/day) (hour/ns) 66: Performance: 17.382 1.381 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.094 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.592 1.446 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.094 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.615 1.444 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (198 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.156 0.078 199.9 66: (ns/day) (hour/ns) 66: Performance: 18.858 1.273 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.089 0.045 199.8 66: (ns/day) (hour/ns) 66: Performance: 17.363 1.382 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.087 0.044 199.8 66: (ns/day) (hour/ns) 66: Performance: 17.771 1.351 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (188 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.072 0.036 199.6 66: (ns/day) (hour/ns) 66: Performance: 40.557 0.592 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.5 66: (ns/day) (hour/ns) 66: Performance: 438.667 0.055 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.0 66: (ns/day) (hour/ns) 66: Performance: 669.848 0.036 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (90 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 194.5 66: (ns/day) (hour/ns) 66: Performance: 995.571 0.024 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.1 66: (ns/day) (hour/ns) 66: Performance: 100.944 0.238 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.8 66: (ns/day) (hour/ns) 66: Performance: 707.022 0.034 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (43 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 190.289 0.126 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.7 66: (ns/day) (hour/ns) 66: Performance: 669.711 0.036 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.6 66: (ns/day) (hour/ns) 66: Performance: 646.608 0.037 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (39 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.7 66: (ns/day) (hour/ns) 66: Performance: 838.404 0.029 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 97.781 0.245 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 100.212 0.239 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (49 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.7 66: (ns/day) (hour/ns) 66: Performance: 880.714 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.0 66: (ns/day) (hour/ns) 66: Performance: 650.996 0.037 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.2 66: (ns/day) (hour/ns) 66: Performance: 610.880 0.039 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (81 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.2 66: (ns/day) (hour/ns) 66: Performance: 188.144 0.128 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 100.196 0.240 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 99.321 0.242 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (158 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 188.952 0.127 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.4 66: (ns/day) (hour/ns) 66: Performance: 95.415 0.252 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.3 66: (ns/day) (hour/ns) 66: Performance: 514.431 0.047 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (69 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.3 66: (ns/day) (hour/ns) 66: Performance: 183.182 0.131 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 193.5 66: (ns/day) (hour/ns) 66: Performance: 563.200 0.043 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 192.9 66: (ns/day) (hour/ns) 66: Performance: 534.583 0.045 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (79 ms) 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1954 ms total) 66: 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.186 0.093 199.8 66: (ns/day) (hour/ns) 66: Performance: 15.759 1.523 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.101 0.051 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.344 1.564 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.101 0.051 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.373 1.561 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (237 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.183 0.092 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.011 1.499 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.101 0.051 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.349 1.564 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.105 0.053 199.7 66: (ns/day) (hour/ns) 66: Performance: 14.760 1.626 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (236 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 196.8 66: (ns/day) (hour/ns) 66: Performance: 735.769 0.033 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.9 66: (ns/day) (hour/ns) 66: Performance: 102.740 0.234 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.003 194.6 66: (ns/day) (hour/ns) 66: Performance: 277.905 0.086 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (37 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 199.1 66: (ns/day) (hour/ns) 66: Performance: 179.819 0.133 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 196.2 66: (ns/day) (hour/ns) 66: Performance: 402.454 0.060 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.011 0.006 197.1 66: (ns/day) (hour/ns) 66: Performance: 135.861 0.177 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (50 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 193.9 66: (ns/day) (hour/ns) 66: Performance: 951.296 0.025 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.0 66: (ns/day) (hour/ns) 66: Performance: 614.217 0.039 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.7 66: (ns/day) (hour/ns) 66: Performance: 615.957 0.039 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (53 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.1 66: (ns/day) (hour/ns) 66: Performance: 183.024 0.131 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.014 0.007 197.7 66: (ns/day) (hour/ns) 66: Performance: 113.530 0.211 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.2 66: (ns/day) (hour/ns) 66: Performance: 615.492 0.039 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (167 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.3 66: (ns/day) (hour/ns) 66: Performance: 860.418 0.028 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 192.3 66: (ns/day) (hour/ns) 66: Performance: 582.721 0.041 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 192.1 66: (ns/day) (hour/ns) 66: Performance: 578.689 0.041 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (56 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 194.0 66: (ns/day) (hour/ns) 66: Performance: 882.354 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.3 66: (ns/day) (hour/ns) 66: Performance: 639.508 0.038 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.0 66: (ns/day) (hour/ns) 66: Performance: 626.006 0.038 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (60 ms) 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (900 ms total) 66: 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.8 66: (ns/day) (hour/ns) 66: Performance: 1765.213 0.014 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 1290.657 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.4 66: (ns/day) (hour/ns) 66: Performance: 1207.512 0.020 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (15 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.1 66: (ns/day) (hour/ns) 66: Performance: 1976.450 0.012 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.2 66: (ns/day) (hour/ns) 66: Performance: 1329.593 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.5 66: (ns/day) (hour/ns) 66: Performance: 1242.946 0.019 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (16 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.122 0.061 199.8 66: (ns/day) (hour/ns) 66: Performance: 24.058 0.998 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.035 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.504 1.066 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 22.563 1.064 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (148 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.114 0.057 199.8 66: (ns/day) (hour/ns) 66: Performance: 25.820 0.930 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.065 0.032 199.6 66: (ns/day) (hour/ns) 66: Performance: 24.022 0.999 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.065 0.033 199.7 66: (ns/day) (hour/ns) 66: Performance: 23.732 1.011 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (140 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.139 0.070 199.9 66: (ns/day) (hour/ns) 66: Performance: 21.131 1.136 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.079 0.039 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.733 1.216 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.7 66: (ns/day) (hour/ns) 66: Performance: 20.345 1.180 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (163 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.131 0.066 199.9 66: (ns/day) (hour/ns) 66: Performance: 22.366 1.073 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 25 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.023 0.012 199.3 66: (ns/day) (hour/ns) 66: Performance: 66.192 0.363 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.5 66: (ns/day) (hour/ns) 66: Performance: 905.718 0.026 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (92 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.8 66: (ns/day) (hour/ns) 66: Performance: 1348.937 0.018 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.3 66: (ns/day) (hour/ns) 66: Performance: 889.659 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 191.3 66: (ns/day) (hour/ns) 66: Performance: 583.242 0.041 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (13 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.009 199.1 66: (ns/day) (hour/ns) 66: Performance: 156.934 0.153 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.5 66: (ns/day) (hour/ns) 66: Performance: 837.999 0.029 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.8 66: (ns/day) (hour/ns) 66: Performance: 830.741 0.029 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (21 ms) 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (613 ms total) 66: 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.014 0.007 198.0 66: (ns/day) (hour/ns) 66: Performance: 212.735 0.113 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 1235.413 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 192.1 66: (ns/day) (hour/ns) 66: Performance: 858.061 0.028 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (18 ms) 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 195.1 66: (ns/day) (hour/ns) 66: Performance: 1151.943 0.021 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.9 66: (ns/day) (hour/ns) 66: Performance: 901.961 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.9 66: (ns/day) (hour/ns) 66: Performance: 880.294 0.027 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (12 ms) 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (31 ms total) 66: 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.009 0.005 198.2 66: (ns/day) (hour/ns) 66: Performance: 318.937 0.075 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.8 66: (ns/day) (hour/ns) 66: Performance: 1229.823 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.7 66: (ns/day) (hour/ns) 66: Performance: 1094.827 0.022 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (19 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.010 0.005 198.3 66: (ns/day) (hour/ns) 66: Performance: 290.814 0.083 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 188.8 66: (ns/day) (hour/ns) 66: Performance: 1200.401 0.020 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.0 66: (ns/day) (hour/ns) 66: Performance: 1168.574 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (16 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 190.3 66: (ns/day) (hour/ns) 66: Performance: 1703.704 0.014 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 1259.749 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.9 66: (ns/day) (hour/ns) 66: Performance: 1158.200 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (16 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 191.2 66: (ns/day) (hour/ns) 66: Performance: 1873.660 0.013 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.7 66: (ns/day) (hour/ns) 66: Performance: 1256.837 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.4 66: (ns/day) (hour/ns) 66: Performance: 1125.040 0.021 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (15 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.3 66: (ns/day) (hour/ns) 66: Performance: 1380.061 0.017 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.7 66: (ns/day) (hour/ns) 66: Performance: 861.688 0.028 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.0 66: (ns/day) (hour/ns) 66: Performance: 835.637 0.029 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (13 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 199.0 66: (ns/day) (hour/ns) 66: Performance: 182.856 0.131 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.0 66: (ns/day) (hour/ns) 66: Performance: 872.756 0.027 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 188.5 66: (ns/day) (hour/ns) 66: Performance: 804.909 0.030 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (23 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.4 66: (ns/day) (hour/ns) 66: Performance: 1245.319 0.019 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 195.0 66: (ns/day) (hour/ns) 66: Performance: 564.272 0.043 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.8 66: (ns/day) (hour/ns) 66: Performance: 787.990 0.030 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (14 ms) 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (118 ms total) 66: 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 66: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.273 0.137 199.9 66: (ns/day) (hour/ns) 66: Performance: 10.760 2.231 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.144 0.072 199.9 66: (ns/day) (hour/ns) 66: Performance: 10.773 2.228 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.142 0.071 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.974 2.187 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (296 ms) 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (296 ms total) 66: 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.140 0.070 199.8 66: (ns/day) (hour/ns) 66: Performance: 21.019 1.142 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.7 66: (ns/day) (hour/ns) 66: Performance: 19.976 1.201 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.6 66: (ns/day) (hour/ns) 66: Performance: 19.944 1.203 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (168 ms) 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.111 0.055 199.8 66: (ns/day) (hour/ns) 66: Performance: 26.473 0.907 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.0 66: (ns/day) (hour/ns) 66: Performance: 814.151 0.029 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.1 66: (ns/day) (hour/ns) 66: Performance: 789.134 0.030 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (70 ms) 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (238 ms total) 66: 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: Setting the AWH bias MC random seed to -603988033 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to -285935617 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.134 0.067 199.7 66: (ns/day) (hour/ns) 66: Performance: 21.882 1.097 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 594.945 0.040 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 190.0 66: (ns/day) (hour/ns) 66: Performance: 583.034 0.041 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (122 ms) 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: Setting the AWH bias MC random seed to -840959041 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to -84285453 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 20 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 198.5 66: (ns/day) (hour/ns) 66: Performance: 101.347 0.237 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 555.431 0.043 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.010 0.005 196.0 66: (ns/day) (hour/ns) 66: Performance: 156.584 0.153 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (64 ms) 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (186 ms total) 66: 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 66: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.006 0.003 197.3 66: (ns/day) (hour/ns) 66: Performance: 472.040 0.051 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.017 0.008 198.9 66: (ns/day) (hour/ns) 66: Performance: 92.003 0.261 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 190.9 66: (ns/day) (hour/ns) 66: Performance: 341.947 0.070 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (59 ms) 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (59 ms total) 66: 66: [----------] 3 tests from Checking/InitialConstraintsTest 66: [ RUN ] Checking/InitialConstraintsTest.Works/0 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1078117003 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 193.5 66: (ns/day) (hour/ns) 66: Performance: 140.189 0.171 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (5 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/1 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 2036332103 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 194.0 66: (ns/day) (hour/ns) 66: Performance: 135.700 0.177 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (8 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: Integrator method md-vv-avek is implemented primarily for validation 66: purposes; for molecular dynamics, you should probably be using md or 66: md-vv 66: 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1208223645 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 185.3 66: (ns/day) (hour/ns) 66: Performance: 318.163 0.075 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (8 ms) 66: [----------] 3 tests from Checking/InitialConstraintsTest (22 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 76 tests from 13 test suites ran. (4803 ms total) 66: [ PASSED ] 76 tests. 66/90 Test #66: MdrunIOTests .............................. Passed 4.82 sec test 67 Start 67: MdrunTestsOneRank 67: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 29 tests from 8 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Generating 1-4 interactions: fudge = 0.5 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -1073873285 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 33 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.284 0.142 199.9 67: (ns/day) (hour/ns) 67: Performance: 9.130 2.629 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 19 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.200 0.100 199.9 67: (ns/day) (hour/ns) 67: Performance: 12.930 1.856 67: [ OK ] CompelTest.SwapCanRun (583 ms) 67: [----------] 1 test from CompelTest (583 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 20 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 184.7 67: (ns/day) (hour/ns) 67: Performance: 513.297 0.047 67: Setting the LD random seed to -1697677601 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalBondWorks (3 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 19 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 184.2 67: (ns/day) (hour/ns) 67: Performance: 455.834 0.053 67: Setting the LD random seed to 515617791 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 21 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 185.9 67: (ns/day) (hour/ns) 67: Performance: 473.091 0.051 67: Setting the LD random seed to -302583833 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (3 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 21 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 186.6 67: (ns/day) (hour/ns) 67: Performance: 486.427 0.049 67: Setting the LD random seed to -9437187 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (3 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 20 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 185.3 67: (ns/day) (hour/ns) 67: Performance: 494.390 0.049 67: Setting the LD random seed to -17875978 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 50 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.054 1.594 67: Setting the LD random seed to 1425336117 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (11 ms) 67: [----------] 6 tests from BondedInteractionsTest (34 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 41 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.014 0.007 198.9 67: (ns/day) (hour/ns) 67: Performance: 24.265 0.989 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -413218 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to -286261922 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (13 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: Setting the LD random seed to -742933298 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.18 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.415 0.208 199.9 67: (ns/day) (hour/ns) 67: Performance: 17.480 1.373 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (502 ms) 67: [----------] 2 tests from BoxDeformationTest (516 ms total) 67: 67: [----------] 1 test from PositionRestraintCommTest 67: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using 67: verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any of the VCM groups 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any center of mass motion removal group. 67: This may lead to artifacts. 67: In most cases one should use one group for the whole system. 67: 67: Number of degrees of freedom in T-Coupling group System is 29527.73 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Channel_coco in octane membrane' 67: 10 steps, 0.0 ps. 67: Setting the LD random seed to -671678482 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.693 0.347 200.0 67: (ns/day) (hour/ns) 67: Performance: 5.482 4.378 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (688 ms) 67: [----------] 1 test from PositionRestraintCommTest (688 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -277506090 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 13 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.105 0.053 199.8 67: (ns/day) (hour/ns) 67: Performance: 8.222 2.919 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -69485139 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 15 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.093 0.047 199.8 67: (ns/day) (hour/ns) 67: Performance: 9.247 2.595 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (155 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 1740627447 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 28 % of the run time was spent in domain decomposition, 67: 10 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.050 0.025 199.4 67: (ns/day) (hour/ns) 67: Performance: 17.312 1.386 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1164443649 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 71 % of the run time was spent in domain decomposition, 67: 1 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 198.3 67: (ns/day) (hour/ns) 67: Performance: 74.701 0.321 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (68 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (223 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1074331953 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 187.1 67: (ns/day) (hour/ns) 67: Performance: 710.286 0.034 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 2129346522 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 187.2 67: (ns/day) (hour/ns) 67: Performance: 659.607 0.036 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (13 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (14 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.014 0.007 198.0 67: (ns/day) (hour/ns) 67: Performance: 112.245 0.214 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (17 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.0 67: (ns/day) (hour/ns) 67: Performance: 798.602 0.030 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (20 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 13 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.092 0.046 199.7 67: (ns/day) (hour/ns) 67: Performance: 16.846 1.425 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (62 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.120 0.060 199.8 67: (ns/day) (hour/ns) 67: Performance: 12.945 1.854 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (75 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.125 0.062 199.8 67: (ns/day) (hour/ns) 67: Performance: 12.473 1.924 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (79 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 67: Parrinello-Rahman is not implemented in md-vv. 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.108 0.054 199.8 67: (ns/day) (hour/ns) 67: Performance: 14.379 1.669 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (72 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.111 0.056 199.8 67: (ns/day) (hour/ns) 67: Performance: 13.947 1.721 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (75 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.109 0.054 199.8 67: (ns/day) (hour/ns) 67: Performance: 14.313 1.677 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (73 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.088 0.044 199.8 67: (ns/day) (hour/ns) 67: Performance: 17.704 1.356 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (78 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.089 0.045 199.8 67: (ns/day) (hour/ns) 67: Performance: 17.407 1.379 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (78 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 190.1 67: (ns/day) (hour/ns) 67: Performance: 901.462 0.027 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (40 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (674 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -2363685 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 190.4 67: (ns/day) (hour/ns) 67: Performance: 2367.688 0.010 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (4 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -159387777 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.007 0.004 196.1 67: (ns/day) (hour/ns) 67: Performance: 410.922 0.058 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (11 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -16945669 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 188.3 67: (ns/day) (hour/ns) 67: Performance: 2722.446 0.009 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (4 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -638687809 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 188.9 67: (ns/day) (hour/ns) 67: Performance: 2275.988 0.011 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (4 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (25 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 29 tests from 8 test suites ran. (2819 ms total) 67: [ PASSED ] 28 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/90 Test #67: MdrunTestsOneRank ......................... Passed 2.84 sec test 68 Start 68: MdrunTestsTwoRanks 68: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 29 tests from 8 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from CompelTest 68: [ RUN ] CompelTest.SwapCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Split0 group 'Ch0' contains 83 atoms. 68: Split1 group 'Ch1' contains 83 atoms. 68: Solvent group 'SOL' contains 11931 atoms. 68: Swap group 'NA+' contains 19 atoms. 68: Swap group 'CL-' contains 19 atoms. 68: Number of degrees of freedom in T-Coupling group System is 27869.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Determining initial numbers of ions per compartment. 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1103382531 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 12.4%. 68: The balanceable part of the MD step is 22%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 2.8%. 68: 68: 68: NOTE: 15 % of the run time was spent in domain decomposition, 68: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.949 0.237 399.8 68: (ns/day) (hour/ns) 68: Performance: 5.463 4.393 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 68: 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Copying channel fluxes from checkpoint file data 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.597 0.399 399.9 68: (ns/day) (hour/ns) 68: Performance: 3.246 7.393 68: [ OK ] CompelTest.SwapCanRun (1217 ms) 68: [----------] 1 test from CompelTest (1217 ms total) 68: 68: [----------] 6 tests from BondedInteractionsTest 68: [ RUN ] BondedInteractionsTest.NormalBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 48 % of the run time was spent in domain decomposition, 68: 8 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.140 0.035 399.8 68: (ns/day) (hour/ns) 68: Performance: 2.473 9.704 68: Setting the LD random seed to 798473719 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalBondWorks (130 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 19 % of the run time was spent in domain decomposition, 68: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 372.5 68: (ns/day) (hour/ns) 68: Performance: 274.849 0.087 68: Setting the LD random seed to 2144141164 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedBondWorks (76 ms) 68: [ RUN ] BondedInteractionsTest.NormalAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 16 % of the run time was spent in domain decomposition, 68: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 372.4 68: (ns/day) (hour/ns) 68: Performance: 281.030 0.085 68: Setting the LD random seed to 1574696428 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalAngleWorks (43 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 19 % of the run time was spent in domain decomposition, 68: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 374.6 68: (ns/day) (hour/ns) 68: Performance: 270.843 0.089 68: Setting the LD random seed to 1928990606 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (67 ms) 68: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 53 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.137 0.034 399.7 68: (ns/day) (hour/ns) 68: Performance: 2.528 9.494 68: Setting the LD random seed to -33817621 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalDihedralWorks (91 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 18 % of the run time was spent in domain decomposition, 68: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 372.7 68: (ns/day) (hour/ns) 68: Performance: 363.114 0.066 68: Setting the LD random seed to -1078469445 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (8 ms) 68: [----------] 6 tests from BondedInteractionsTest (419 ms total) 68: 68: [----------] 2 tests from BoxDeformationTest 68: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 0 steps, 0.0 ps. 68: 68: NOTE: 20 % of the run time was spent in domain decomposition, 68: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 292.6 68: (ns/day) (hour/ns) 68: Performance: 960.604 0.025 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1994905599 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Setting gen_seed to 1811675131 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (24 ms) 68: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 1293.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 20 steps, 0.0 ps. 68: Setting the LD random seed to 1988089399 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 68: 68: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 68: 68: Estimate for the relative computational load of the PME mesh part: 0.18 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.9%. 68: The balanceable part of the MD step is 46%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.4%. 68: 68: 68: NOTE: 8 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.095 0.024 398.6 68: (ns/day) (hour/ns) 68: Performance: 152.850 0.157 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (324 ms) 68: [----------] 2 tests from BoxDeformationTest (348 ms total) 68: 68: [----------] 1 test from PositionRestraintCommTest 68: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using 68: verlet-buffer-tolerance. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any of the VCM groups 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any center of mass motion removal group. 68: This may lead to artifacts. 68: In most cases one should use one group for the whole system. 68: 68: Number of degrees of freedom in T-Coupling group System is 29527.73 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Channel_coco in octane membrane' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to -336597116 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.707 0.427 399.9 68: (ns/day) (hour/ns) 68: Performance: 4.453 5.389 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1104 ms) 68: [----------] 1 test from PositionRestraintCommTest (1104 ms total) 68: 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -1627407109 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 32 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.013 397.2 68: (ns/day) (hour/ns) 68: Performance: 34.474 0.696 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2004022771 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 5 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.134 0.034 399.0 68: (ns/day) (hour/ns) 68: Performance: 12.823 1.872 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 68: 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (591 ms) 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -671097921 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 50 % of the run time was spent in domain decomposition, 68: 2 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.869 0.217 399.9 68: (ns/day) (hour/ns) 68: Performance: 1.989 12.066 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -206119683 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 26 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 2.017 0.504 399.9 68: (ns/day) (hour/ns) 68: Performance: 0.857 28.013 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (972 ms) 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1564 ms total) 68: 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -1214267409 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 46 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.004 391.4 68: (ns/day) (hour/ns) 68: Performance: 107.454 0.223 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2130427903 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 46 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.004 390.8 68: (ns/day) (hour/ns) 68: Performance: 111.429 0.215 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (520 ms) 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (520 ms total) 68: 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 36.3%. 68: The balanceable part of the MD step is 46%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 16.8%. 68: 68: NOTE: 16.8 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 9 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.744 0.188 395.7 68: (ns/day) (hour/ns) 68: Performance: 4.136 5.803 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (236 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 18.1%. 68: The balanceable part of the MD step is 39%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 7.0%. 68: 68: NOTE: 7.0 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 26 % of the run time was spent in domain decomposition, 68: 1 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 7 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.330 0.333 399.5 68: (ns/day) (hour/ns) 68: Performance: 2.336 10.275 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (425 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 4.1%. 68: The balanceable part of the MD step is 27%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 1.1%. 68: 68: 68: NOTE: 25 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 9 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.315 0.079 399.8 68: (ns/day) (hour/ns) 68: Performance: 9.855 2.435 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (426 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 19.8%. 68: The balanceable part of the MD step is 42%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 8.3%. 68: 68: NOTE: 8.3 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.159 0.040 399.1 68: (ns/day) (hour/ns) 68: Performance: 19.470 1.233 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (91 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 2.0%. 68: The balanceable part of the MD step is 57%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 1.2%. 68: 68: 68: NOTE: 19 % of the run time was spent in domain decomposition, 68: 8 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 6 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.485 0.121 399.8 68: (ns/day) (hour/ns) 68: Performance: 6.412 3.743 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (191 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 68: Parrinello-Rahman is not implemented in md-vv. 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in domain decomposition, 68: 6 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.303 0.076 398.6 68: (ns/day) (hour/ns) 68: Performance: 10.226 2.347 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (229 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 57 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 15 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.381 0.095 399.7 68: (ns/day) (hour/ns) 68: Performance: 8.158 2.942 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (694 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 5 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.170 0.293 399.7 68: (ns/day) (hour/ns) 68: Performance: 2.657 9.031 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (411 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 38 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.012 334.5 68: (ns/day) (hour/ns) 68: Performance: 66.604 0.360 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (465 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 8 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.875 0.220 397.2 68: (ns/day) (hour/ns) 68: Performance: 3.530 6.799 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (371 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 52 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 14 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.129 0.034 379.8 68: (ns/day) (hour/ns) 68: Performance: 22.920 1.047 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (106 ms) 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest (3651 ms total) 68: 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 536736763 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.7%. 68: The balanceable part of the MD step is 35%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.2%. 68: 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.020 398.4 68: (ns/day) (hour/ns) 68: Performance: 77.107 0.311 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (33 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -574623783 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 2.3%. 68: The balanceable part of the MD step is 30%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.7%. 68: 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.127 0.032 399.0 68: (ns/day) (hour/ns) 68: Performance: 48.674 0.493 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (91 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -471335426 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.1%. 68: The balanceable part of the MD step is 42%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.0%. 68: 68: 68: NOTE: 58 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.015 397.8 68: (ns/day) (hour/ns) 68: Performance: 106.443 0.225 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (24 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -134758409 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 1.0%. 68: The balanceable part of the MD step is 51%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.5%. 68: 68: 68: NOTE: 21 % of the run time was spent in domain decomposition, 68: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.340 0.085 399.7 68: (ns/day) (hour/ns) 68: Performance: 18.269 1.314 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (122 ms) 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (271 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 29 tests from 8 test suites ran. (9162 ms total) 68: [ PASSED ] 28 tests. 68: [ SKIPPED ] 1 test, listed below: 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68/90 Test #68: MdrunTestsTwoRanks ........................ Passed 9.19 sec test 69 Start 69: MdrunSingleRankAlgorithmsTests 69: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 5 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from DispersionCorrectionTest 69: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 30.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 200 steps, 0.4 ps. 69: Setting the LD random seed to -25691011 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 3 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 12 Constraints with virtual sites to connections, 0 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.029 0.015 199.4 69: (ns/day) (hour/ns) 69: Performance: 2348.615 0.010 69: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (44 ms) 69: [----------] 1 test from DispersionCorrectionTest (44 ms total) 69: 69: [----------] 1 test from OriresTest 69: [ RUN ] OriresTest.OriresCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 518.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 69: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 69: 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to -20971649 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.016 0.008 198.3 69: (ns/day) (hour/ns) 69: Performance: 239.430 0.100 69: [ OK ] OriresTest.OriresCanRun (321 ms) 69: [----------] 1 test from OriresTest (321 ms total) 69: 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 69: Number of degrees of freedom in T-Coupling group rest is 10.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -4653223 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: Searching the wall atom type(s) 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.8 69: (ns/day) (hour/ns) 69: Performance: 409.526 0.059 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 69: 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (28 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 69: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 69: The supported numbers are > 1. 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 all molecules should be neutral. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 you can only use domain decomposition when there 69: are only small molecules with all bonds constrained (mdrun will check for 69: this). 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to 2145361374 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.008 0.004 197.6 69: (ns/day) (hour/ns) 69: Performance: 1093.098 0.022 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (12 ms) 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (41 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 5 tests from 3 test suites ran. (433 ms total) 69: [ PASSED ] 5 tests. 69/90 Test #69: MdrunSingleRankAlgorithmsTests ............ Passed 0.45 sec test 70 Start 70: Minimize1RankTests 70: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.79910463671092e+01 70: Maximum force = 1.86297359432231e+02 on atom 13 70: Norm of force = 8.77219865482157e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (270 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.58622538633302e+01 70: Maximum force = 4.27274822366368e+02 on atom 13 70: Norm of force = 1.84530029253754e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (287 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.19376899751523e+02 70: Maximum force = 9.99884921009767e+03 on atom 9 70: Norm of force = 4.61669565054298e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (68 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.51743018140928e+02 70: Maximum force = 7.42089573409108e+03 on atom 9 70: Norm of force = 3.56929298615740e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (67 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.56984193848274e+02 70: Maximum force = 4.56923624626570e+02 on atom 17 70: Norm of force = 1.83258377168389e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (12 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06800e+03 on atom 28 70: F-Norm = 4.26922e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.69410778678181e+02 70: Maximum force = 2.18225948473987e+02 on atom 17 70: Norm of force = 7.92068036537548e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (12 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (718 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.74257075835447e-01 70: Maximum force = 4.01322929015133e+00 on atom 1 70: Norm of force = 1.63839399694378e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (7 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.90642313893957e-01 70: Maximum force = 2.57812909491104e+00 on atom 1 70: Norm of force = 1.05251679559258e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 70: Potential Energy = -9.90642313893957e-01 70: Maximum force = 2.57812909491104e+00 on atom 1 70: Norm of force = 1.05251679559258e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.19395484891520e+02 70: Maximum force = 9.97041707197911e+03 on atom 9 70: Norm of force = 4.62274878665467e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (67 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.56258793899480e+02 70: Maximum force = 7.50181017480397e+03 on atom 9 70: Norm of force = 3.61390332564874e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (67 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization has stopped, but the forces have not converged to the 70: requested precision Fmax < 10 (which may not be possible for your system). It 70: stopped because the algorithm tried to make a new step whose size was too 70: small, or there was no change in the energy since last step. Either way, we 70: regard the minimization as converged to within the available machine 70: precision, given your starting configuration and EM parameters. 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 70: but did not reach the requested Fmax < 10. 70: Potential Energy = 5.61116097794205e+02 70: Maximum force = 1.26854826291223e+04 on atom 10 70: Norm of force = 6.06436286976271e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (63 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (219 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (954 ms total) 70: [ PASSED ] 12 tests. 70/90 Test #70: Minimize1RankTests ........................ Passed 0.97 sec test 71 Start 71: Minimize2RankTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 12 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -4.79910463671093e+01 71: Maximum force = 1.86297359432232e+02 on atom 13 71: Norm of force = 8.77219865482159e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (669 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 3.02331e+02 on atom 3 71: F-Norm = 1.18024e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -5.58622538633302e+01 71: Maximum force = 4.27274822366367e+02 on atom 13 71: Norm of force = 1.84530029253753e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (704 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.19376899751523e+02 71: Maximum force = 9.99884921009767e+03 on atom 9 71: Norm of force = 4.61669565054298e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (572 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: 71: NOTE 3 [file glycine_vacuo.top, line 12]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41575e+04 on atom 10 71: F-Norm = 1.18451e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.51743018140927e+02 71: Maximum force = 7.42089573409111e+03 on atom 9 71: Norm of force = 3.56929298615739e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (383 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.56984193848274e+02 71: Maximum force = 4.56923624626570e+02 on atom 17 71: Norm of force = 1.83258377168389e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (572 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: 71: NOTE 4 [file unknown]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 6 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 1.06800e+03 on atom 28 71: F-Norm = 4.26922e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.69410778678181e+02 71: Maximum force = 2.18225948473987e+02 on atom 17 71: Norm of force = 7.92068036537548e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (190 ms) 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3092 ms total) 71: 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents converged to Fmax < 10 in 1 steps 71: Potential Energy = -9.74257075835447e-01 71: Maximum force = 4.01322929015133e+00 on atom 3 71: Norm of force = 1.63839399694378e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (293 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 4.01323e+00 on atom 3 71: F-Norm = 1.63839e+00 71: 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 71: Potential Energy = -9.90642313893957e-01 71: Maximum force = 2.57812909491104e+00 on atom 3 71: Norm of force = 1.05251679559258e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (44 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: 71: There was 1 WARNING 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.19395484891520e+02 71: Maximum force = 9.97041707197911e+03 on atom 9 71: Norm of force = 4.62274878665467e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (83 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41672e+04 on atom 10 71: F-Norm = 1.19357e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.56258793899480e+02 71: Maximum force = 7.50181017480397e+03 on atom 9 71: Norm of force = 3.61390332564874e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (86 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (61 ms) 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (572 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 2 test suites ran. (3678 ms total) 71: [ PASSED ] 12 tests. 71/90 Test #71: Minimize2RankTests ........................ Passed 3.70 sec test 72 Start 72: MdrunNonIntegratorTests 72: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 53 tests from 5 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from NonbondedBenchTest 72: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 72: SIMD width: 2 72: System size: 3000 atoms 72: Cut-off radius: 1 nm 72: Number of threads: 1 72: Number of iterations: 1 72: Compute energies: no 72: Ewald excl. corr.: analytical 72: 72: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 72: total useful 72: Ewald all geom. 4xM 0.234 0.2337 4.5349 2.6952 72: [ OK ] NonbondedBenchTest.BasicEndToEndTest (27 ms) 72: [----------] 1 test from NonbondedBenchTest (27 ms total) 72: 72: [----------] 5 tests from NormalModesWorks/NormalModesTest 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation '2 scaled waters' 72: 12 steps. 72: 72: Maximum force: 9.96989e-06 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (20 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file villin.top, line 2452]: 72: System has non-zero total charge: -2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group System is 765.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=256), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 72: 512 steps. 72: 72: Maximum force: 6.97568e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 50... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--50 to eigenvec.trr 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 256 Atoms 72: Using begin = 7 and end = 50 72: Full matrix storage format, nrow=768, ncols=768 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (1715 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'flex spc dimer' 72: 12 steps. 72: 72: Maximum force: 3.36401e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (284 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 6.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=3), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation '1 TIP5P' 72: 6 steps. 72: 72: Maximum force: 2.42882e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 9... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--9 to eigenvec.trr 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: This run will generate roughly 0 Mb of data 72: There are: 3 Atoms 72: There are: 2 VSites 72: Using begin = 7 and end = 9 72: Full matrix storage format, nrow=9, ncols=9 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (278 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'sw dimer' 72: 12 steps. 72: 72: Maximum force: 1.07599e-03 72: The force is probably not small enough to ensure that you are at a minimum. 72: Be aware that negative eigenvalues may occur 72: when the resulting matrix is diagonalized. 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 6 of the 10 non-bonded parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SW' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: There are: 2 Shells 72: There are: 2 VSites 72: 72: NOTE: in the current version shell prediction during the crun is disabled 72: 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (9 ms) 72: [----------] 5 tests from NormalModesWorks/NormalModesTest (2309 ms total) 72: 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.007 0.004 196.6 72: (ns/day) (hour/ns) 72: Performance: 389.049 0.062 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 72: 72: trr version: GMX_trn_file (double precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 189.9 72: (ns/day) (hour/ns) 72: Performance: 4311.122 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (12 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.016 0.008 199.2 72: (ns/day) (hour/ns) 72: Performance: 184.267 0.130 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 190.6 72: (ns/day) (hour/ns) 72: Performance: 4526.520 0.005 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (16 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 197.9 72: (ns/day) (hour/ns) 72: Performance: 250.685 0.096 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 190.0 72: (ns/day) (hour/ns) 72: Performance: 3933.968 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (18 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1971.390 0.012 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 191.0 72: (ns/day) (hour/ns) 72: Performance: 4335.393 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (10 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.015 0.008 198.3 72: (ns/day) (hour/ns) 72: Performance: 188.507 0.127 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 191.3 72: (ns/day) (hour/ns) 72: Performance: 4005.588 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (311 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 196.2 72: (ns/day) (hour/ns) 72: Performance: 864.645 0.028 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 188.9 72: (ns/day) (hour/ns) 72: Performance: 3466.851 0.007 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (310 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.004 197.0 72: (ns/day) (hour/ns) 72: Performance: 363.457 0.066 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 190.2 72: (ns/day) (hour/ns) 72: Performance: 3675.772 0.007 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (312 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 1506.626 0.016 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.000 191.6 72: (ns/day) (hour/ns) 72: Performance: 3855.190 0.006 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (305 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.015 0.008 198.2 72: (ns/day) (hour/ns) 72: Performance: 190.548 0.126 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.9 72: (ns/day) (hour/ns) 72: Performance: 2449.540 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (24 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 195.1 72: (ns/day) (hour/ns) 72: Performance: 745.925 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 193.3 72: (ns/day) (hour/ns) 72: Performance: 2483.109 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (16 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.016 0.008 198.4 72: (ns/day) (hour/ns) 72: Performance: 187.789 0.128 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.4 72: (ns/day) (hour/ns) 72: Performance: 2301.305 0.010 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (93 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 197.6 72: (ns/day) (hour/ns) 72: Performance: 290.539 0.083 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 2256.628 0.011 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (52 ms) 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1484 ms total) 72: 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.0 72: (ns/day) (hour/ns) 72: Performance: 923.074 0.026 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 12 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 192.8 72: (ns/day) (hour/ns) 72: Performance: 1226.233 0.020 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (24 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.6 72: (ns/day) (hour/ns) 72: Performance: 976.787 0.025 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.8 72: (ns/day) (hour/ns) 72: Performance: 1879.949 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 192.9 72: (ns/day) (hour/ns) 72: Performance: 933.989 0.026 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 193.1 72: (ns/day) (hour/ns) 72: Performance: 1261.641 0.019 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (23 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.4 72: (ns/day) (hour/ns) 72: Performance: 925.848 0.026 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 198.2 72: (ns/day) (hour/ns) 72: Performance: 293.529 0.082 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (27 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.7 72: (ns/day) (hour/ns) 72: Performance: 987.591 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.0 72: (ns/day) (hour/ns) 72: Performance: 1992.430 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (16 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 192.9 72: (ns/day) (hour/ns) 72: Performance: 967.886 0.025 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 198.2 72: (ns/day) (hour/ns) 72: Performance: 295.288 0.081 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (27 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.0 72: (ns/day) (hour/ns) 72: Performance: 992.683 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 190.3 72: (ns/day) (hour/ns) 72: Performance: 1728.562 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 192.7 72: (ns/day) (hour/ns) 72: Performance: 992.044 0.024 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1993.720 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (16 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 192.7 72: (ns/day) (hour/ns) 72: Performance: 954.095 0.025 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.0 72: (ns/day) (hour/ns) 72: Performance: 1953.264 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.181 0.091 199.8 72: (ns/day) (hour/ns) 72: Performance: 16.196 1.482 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 55 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.059 0.030 199.7 72: (ns/day) (hour/ns) 72: Performance: 49.360 0.486 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (143 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.181 0.091 199.9 72: (ns/day) (hour/ns) 72: Performance: 16.196 1.482 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 55 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.060 0.030 199.7 72: (ns/day) (hour/ns) 72: Performance: 49.123 0.489 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (146 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.229 0.115 199.9 72: (ns/day) (hour/ns) 72: Performance: 12.801 1.875 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 55 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.013 0.006 198.8 72: (ns/day) (hour/ns) 72: Performance: 232.677 0.103 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (140 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.3 72: (ns/day) (hour/ns) 72: Performance: 744.843 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.2 72: (ns/day) (hour/ns) 72: Performance: 1972.652 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.3 72: (ns/day) (hour/ns) 72: Performance: 765.576 0.031 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1922.182 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (23 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.2 72: (ns/day) (hour/ns) 72: Performance: 770.170 0.031 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.5 72: (ns/day) (hour/ns) 72: Performance: 2038.582 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.2 72: (ns/day) (hour/ns) 72: Performance: 737.178 0.033 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.2 72: (ns/day) (hour/ns) 72: Performance: 1741.264 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (27 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.5 72: (ns/day) (hour/ns) 72: Performance: 740.367 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.4 72: (ns/day) (hour/ns) 72: Performance: 1952.026 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (20 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.3 72: (ns/day) (hour/ns) 72: Performance: 749.373 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.8 72: (ns/day) (hour/ns) 72: Performance: 1947.706 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (19 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.5 72: (ns/day) (hour/ns) 72: Performance: 745.383 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.1 72: (ns/day) (hour/ns) 72: Performance: 1919.188 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (23 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.1 72: (ns/day) (hour/ns) 72: Performance: 747.282 0.032 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.053 0.027 199.7 72: (ns/day) (hour/ns) 72: Performance: 54.947 0.437 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (47 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.004 198.2 72: (ns/day) (hour/ns) 72: Performance: 344.629 0.070 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.7 72: (ns/day) (hour/ns) 72: Performance: 1911.447 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (28 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 196.7 72: (ns/day) (hour/ns) 72: Performance: 778.344 0.031 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 1967.612 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (23 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.4 72: (ns/day) (hour/ns) 72: Performance: 887.694 0.027 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 192.0 72: (ns/day) (hour/ns) 72: Performance: 1885.704 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (30 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.9 72: (ns/day) (hour/ns) 72: Performance: 868.301 0.028 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 190.9 72: (ns/day) (hour/ns) 72: Performance: 1712.227 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (37 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.5 72: (ns/day) (hour/ns) 72: Performance: 876.953 0.027 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.4 72: (ns/day) (hour/ns) 72: Performance: 1855.601 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (31 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.4 72: (ns/day) (hour/ns) 72: Performance: 876.329 0.027 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 191.3 72: (ns/day) (hour/ns) 72: Performance: 1923.983 0.012 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (34 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.8 72: (ns/day) (hour/ns) 72: Performance: 854.570 0.028 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 190.9 72: (ns/day) (hour/ns) 72: Performance: 1877.085 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (33 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.7 72: (ns/day) (hour/ns) 72: Performance: 873.471 0.027 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 192.1 72: (ns/day) (hour/ns) 72: Performance: 1681.844 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (35 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.9 72: (ns/day) (hour/ns) 72: Performance: 894.525 0.027 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.4 72: (ns/day) (hour/ns) 72: Performance: 1862.332 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (32 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.8 72: (ns/day) (hour/ns) 72: Performance: 838.632 0.029 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 1875.942 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (38 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.1 72: (ns/day) (hour/ns) 72: Performance: 866.591 0.028 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.3 72: (ns/day) (hour/ns) 72: Performance: 1788.790 0.013 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (34 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.215 0.107 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.681 1.754 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 51 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.064 0.032 199.7 72: (ns/day) (hour/ns) 72: Performance: 45.916 0.523 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (172 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.214 0.107 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.738 1.747 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.064 0.032 199.7 72: (ns/day) (hour/ns) 72: Performance: 45.773 0.524 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (171 ms) 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1537 ms total) 72: 72: [----------] 2 tests from Angles1/SimpleMdrunTest 72: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file angles1.top, line 72]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group System is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 238.919 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'This_incredible_box_of_butane' 72: 50 steps, 0.1 ps. 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/angles1.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.055 0.028 199.5 72: (ns/day) (hour/ns) 72: Performance: 158.799 0.151 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 72: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (37 ms) 72: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file angles1.top, line 72]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group System is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 238.919 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'This_incredible_box_of_butane' 72: 50 steps, 0.1 ps. 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/angles1.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.309 0.155 200.0 72: (ns/day) (hour/ns) 72: Performance: 28.505 0.842 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 72: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (162 ms) 72: [----------] 2 tests from Angles1/SimpleMdrunTest (199 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 53 tests from 5 test suites ran. (5588 ms total) 72: [ PASSED ] 53 tests. 72/90 Test #72: MdrunNonIntegratorTests ................... Passed 5.60 sec test 73 Start 73: MdrunTpiTests 73: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 3 tests from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 3 tests from Simple/TpiTest 73: [ RUN ] Simple/TpiTest.ReproducesOutput/0 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/0 (294 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/1 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/1 (263 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/2 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/2 (271 ms) 73: [----------] 3 tests from Simple/TpiTest (830 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 3 tests from 1 test suite ran. (838 ms total) 73: [ PASSED ] 3 tests. 73/90 Test #73: MdrunTpiTests ............................. Passed 0.85 sec test 74 Start 74: MdrunMpiTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 16 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from MimicTest 74: [ RUN ] MimicTest.OneQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 52 % of the run time was spent in domain decomposition, 74: 33 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.057 0.014 399.4 74: (ns/day) (hour/ns) 74: Performance: 6.035 3.977 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1576691623 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.OneQuantumMol (297 ms) 74: [ RUN ] MimicTest.AllQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 80 % of the run time was spent in domain decomposition, 74: 9 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.208 0.052 399.8 74: (ns/day) (hour/ns) 74: Performance: 1.663 14.432 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -268441393 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.AllQuantumMol (128 ms) 74: [ RUN ] MimicTest.TwoQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 74 % of the run time was spent in domain decomposition, 74: 9 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.128 0.032 399.7 74: (ns/day) (hour/ns) 74: Performance: 2.698 8.895 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1056960491 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.TwoQuantumMol (91 ms) 74: [ RUN ] MimicTest.BondCuts 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 66.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: NVE simulation: will use the initial temperature of 300.368 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 74 % of the run time was spent in domain decomposition, 74: 7 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.149 0.037 399.7 74: (ns/day) (hour/ns) 74: Performance: 2.321 10.339 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -426774667 74: 74: Generated 2211 of the 2211 non-bonded parameter combinations 74: 74: Generated 2211 of the 2211 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.BondCuts (123 ms) 74: [----------] 4 tests from MimicTest (642 ms total) 74: 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: There was 1 NOTE 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There was 1 NOTE 74: Setting the LD random seed to -272732233 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -1111787729 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to 935026687 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -806424881 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 0.4%. 74: The balanceable part of the MD step is 50%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.2%. 74: 74: 74: NOTE: 17 % of the run time was spent in domain decomposition, 74: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 9 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.592 0.148 399.5 74: (ns/day) (hour/ns) 74: Performance: 12.253 1.959 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (401 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 16 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 2.518 0.630 399.8 74: (ns/day) (hour/ns) 74: Performance: 2.881 8.330 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (719 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 0.1%. 74: The balanceable part of the MD step is 25%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.0%. 74: 74: 74: NOTE: 22 % of the run time was spent in domain decomposition, 74: 3 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.316 0.329 399.9 74: (ns/day) (hour/ns) 74: Performance: 5.513 4.354 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (353 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 2.067 0.517 400.0 74: (ns/day) (hour/ns) 74: Performance: 3.511 6.836 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (581 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 2.607 0.652 399.8 74: (ns/day) (hour/ns) 74: Performance: 2.783 8.625 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (728 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 1.785 0.446 399.9 74: (ns/day) (hour/ns) 74: Performance: 4.065 5.904 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (477 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (3262 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 16 tests from 2 test suites ran. (3929 ms total) 74: [ PASSED ] 10 tests. 74: [ SKIPPED ] 6 tests, listed below: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74/90 Test #74: MdrunMpiTests ............................. Passed 3.95 sec test 75 Start 75: MdrunMultiSimTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 2 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 2 tests from InNvt/MultiSimTerminationTest 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 75: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 2 tests from 1 test suite ran. (7 ms total) 75: [ PASSED ] 2 tests. 75: 75: YOU HAVE 4 DISABLED TESTS 75: 75/90 Test #75: MdrunMultiSimTests ........................ Passed 0.02 sec test 76 Start 76: MdrunMultiSimReplexTests 76: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 1 test from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 76: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 76: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 1 test from 1 test suite ran. (7 ms total) 76: [ PASSED ] 1 test. 76: 76: YOU HAVE 4 DISABLED TESTS 76: 76/90 Test #76: MdrunMultiSimReplexTests .................. Passed 0.02 sec test 77 Start 77: MdrunMultiSimReplexEquivalenceTests 77: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 0 tests from 0 test suites. 77: [==========] 0 tests from 0 test suites ran. (0 ms total) 77: [ PASSED ] 0 tests. 77: 77: YOU HAVE 10 DISABLED TESTS 77: 77/90 Test #77: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.01 sec test 78 Start 78: MdrunMpi1RankPmeTests 78: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -201721861 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to 1874287039 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 199.2 78: (ns/day) (hour/ns) 78: Performance: 170.371 0.141 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (92 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.009 199.2 78: (ns/day) (hour/ns) 78: Performance: 193.411 0.124 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (13 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.013 0.006 198.0 78: (ns/day) (hour/ns) 78: Performance: 13.652 1.758 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (19 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 199.0 78: (ns/day) (hour/ns) 78: Performance: 150.956 0.159 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (16 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (143 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (157 ms total) 78: [ PASSED ] 4 tests. 78: [ SKIPPED ] 15 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78/90 Test #78: MdrunMpi1RankPmeTests ..................... Passed 0.17 sec test 79 Start 79: MdrunMpi2RankPmeTests 79: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 19 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 19 tests from ReproducesEnergies/PmeTest 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 13.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 966.268 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -2697638 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -1076167843 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Searching the wall atom type(s) 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 11.8%. 79: The balanceable part of the MD step is 10%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 1.1%. 79: 79: 79: NOTE: 32 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.075 0.019 398.4 79: (ns/day) (hour/ns) 79: Performance: 96.745 0.248 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (78 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 9.4%. 79: The balanceable part of the MD step is 1%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.1%. 79: 79: 79: NOTE: 41 % of the run time was spent in domain decomposition, 79: 0 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.218 0.055 399.6 79: (ns/day) (hour/ns) 79: Performance: 33.216 0.723 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (244 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.001 374.4 79: (ns/day) (hour/ns) 79: Performance: 70.751 0.339 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (96 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.303 0.076 399.6 79: (ns/day) (hour/ns) 79: Performance: 23.900 1.004 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (638 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.519 0.130 399.8 79: (ns/day) (hour/ns) 79: Performance: 13.977 1.717 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (155 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 32 % of the run time was spent in domain decomposition, 79: 7 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.062 0.016 396.1 79: (ns/day) (hour/ns) 79: Performance: 5.516 4.351 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (59 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 4.0%. 79: The balanceable part of the MD step is 19%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.7%. 79: 79: 79: NOTE: 9 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 2.264 0.566 400.0 79: (ns/day) (hour/ns) 79: Performance: 3.205 7.489 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (872 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [----------] 19 tests from ReproducesEnergies/PmeTest (2146 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 19 tests from 1 test suite ran. (2160 ms total) 79: [ PASSED ] 7 tests. 79: [ SKIPPED ] 12 tests, listed below: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79/90 Test #79: MdrunMpi2RankPmeTests ..................... Passed 2.17 sec test 80 Start 80: MdrunCoordinationBasicTests1Rank 80: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.002 98.1 80: (ns/day) (hour/ns) 80: Performance: 908.508 0.026 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 96.4 80: (ns/day) (hour/ns) 80: Performance: 2233.718 0.011 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.7 80: (ns/day) (hour/ns) 80: Performance: 2679.684 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.4 80: (ns/day) (hour/ns) 80: Performance: 2574.423 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.7 80: (ns/day) (hour/ns) 80: Performance: 2560.513 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 95.7 80: (ns/day) (hour/ns) 80: Performance: 2578.733 0.009 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (28 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (29 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (36 ms total) 80: [ PASSED ] 1 test. 80/90 Test #80: MdrunCoordinationBasicTests1Rank .......... Passed 0.05 sec test 81 Start 81: MdrunCoordinationBasicTests2Ranks 81: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 1 test from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest 81: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.6%. 81: The balanceable part of the MD step is 54%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 37 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 195.5 81: (ns/day) (hour/ns) 81: Performance: 682.993 0.035 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.7%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 26 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.002 0.001 191.4 81: (ns/day) (hour/ns) 81: Performance: 1678.636 0.014 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.1%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 27 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 190.2 81: (ns/day) (hour/ns) 81: Performance: 1919.188 0.013 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.8%. 81: The balanceable part of the MD step is 43%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.2%. 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.002 0.001 189.5 81: (ns/day) (hour/ns) 81: Performance: 1741.264 0.014 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 3.1%. 81: The balanceable part of the MD step is 43%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.3%. 81: 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.002 0.001 190.4 81: (ns/day) (hour/ns) 81: Performance: 1845.594 0.013 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.5%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.1%. 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.002 0.001 190.2 81: (ns/day) (hour/ns) 81: Performance: 1814.074 0.013 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (85 ms) 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest (85 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 1 test from 1 test suite ran. (93 ms total) 81: [ PASSED ] 1 test. 81/90 Test #81: MdrunCoordinationBasicTests2Ranks ......... Passed 0.11 sec test 82 Start 82: MdrunCoordinationCouplingTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.006 0.006 99.4 82: (ns/day) (hour/ns) 82: Performance: 248.822 0.096 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2395.254 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.000 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2848.171 0.008 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2574.423 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2665.770 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2734.396 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (31 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 1952.645 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2351.372 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2483.109 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 1766.732 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 23 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 1830.242 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2485.112 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1966.356 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2284.239 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2593.934 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2469.176 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.7 82: (ns/day) (hour/ns) 82: Performance: 2427.342 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2496.189 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1966.984 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1828.612 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2632.732 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2508.385 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2466.210 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2550.970 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2056.273 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2463.252 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2746.587 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2512.477 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2442.741 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 1810.874 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1935.468 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2258.282 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2672.709 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2494.167 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2447.594 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2329.147 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1577.617 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2313.404 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2601.602 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2435.017 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2473.141 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2561.577 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1965.729 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2226.452 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 1995.657 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.0 82: (ns/day) (hour/ns) 82: Performance: 2446.622 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2471.157 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2531.057 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 2079.174 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2401.791 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2777.545 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2471.157 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1969.499 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2434.055 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 1976.450 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2251.679 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2554.143 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2130.219 0.011 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2479.112 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2545.700 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (32 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1939.734 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2306.475 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2665.770 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.3 82: (ns/day) (hour/ns) 82: Performance: 2658.867 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2521.733 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.9 82: (ns/day) (hour/ns) 82: Performance: 2572.273 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1568.379 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 1916.800 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2613.744 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2539.404 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2510.429 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2548.860 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.9 82: (ns/day) (hour/ns) 82: Performance: 2043.315 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 2415.919 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2736.825 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2565.845 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 2420.666 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1984.727 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1878.803 0.013 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 2337.099 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2623.762 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2512.477 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2485.112 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 2345.999 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.9 82: (ns/day) (hour/ns) 82: Performance: 1579.234 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 2307.338 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2581.976 0.009 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2370.371 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2485.112 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2371.283 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (26 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1966.356 0.012 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2316.013 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1961.973 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2298.729 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2466.210 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2452.466 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.6 82: (ns/day) (hour/ns) 82: Performance: 1642.387 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1769.269 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.3 82: (ns/day) (hour/ns) 82: Performance: 2050.114 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1481.624 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.8 82: (ns/day) (hour/ns) 82: Performance: 1553.352 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1904.357 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.7 82: (ns/day) (hour/ns) 82: Performance: 1577.213 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1749.672 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1965.102 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1803.981 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1494.202 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.9 82: (ns/day) (hour/ns) 82: Performance: 993.164 0.024 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.9 82: (ns/day) (hour/ns) 82: Performance: 1552.178 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.3 82: (ns/day) (hour/ns) 82: Performance: 1724.690 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1893.237 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.5 82: (ns/day) (hour/ns) 82: Performance: 1799.764 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.4 82: (ns/day) (hour/ns) 82: Performance: 1744.222 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1440.738 0.017 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (27 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1628.064 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1822.661 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1988.571 0.012 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1866.281 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1819.431 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.2 82: (ns/day) (hour/ns) 82: Performance: 1837.338 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (28 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1450.234 0.017 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.0 82: (ns/day) (hour/ns) 82: Performance: 1690.149 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1824.280 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.1 82: (ns/day) (hour/ns) 82: Performance: 1427.385 0.017 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1758.160 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.0 82: (ns/day) (hour/ns) 82: Performance: 1832.965 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (28 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1487.348 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1759.164 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 1479.489 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.0 82: (ns/day) (hour/ns) 82: Performance: 1484.480 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1713.180 0.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1807.686 0.013 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (32 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1412.980 0.017 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 86.2 82: (ns/day) (hour/ns) 82: Performance: 1302.727 0.018 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1338.677 0.018 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1559.644 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1619.504 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1606.413 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (29 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.002 97.1 82: (ns/day) (hour/ns) 82: Performance: 964.250 0.025 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.7 82: (ns/day) (hour/ns) 82: Performance: 1230.396 0.020 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.3 82: (ns/day) (hour/ns) 82: Performance: 1311.881 0.018 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1050.400 0.023 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1249.867 0.019 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.5 82: (ns/day) (hour/ns) 82: Performance: 1255.982 0.019 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (30 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 97.2 82: (ns/day) (hour/ns) 82: Performance: 1374.212 0.017 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1206.068 0.020 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 1593.944 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.8 82: (ns/day) (hour/ns) 82: Performance: 1571.981 0.015 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.4 82: (ns/day) (hour/ns) 82: Performance: 1499.293 0.016 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.6 82: (ns/day) (hour/ns) 82: Performance: 1269.440 0.019 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (29 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (701 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (709 ms total) 82: [ PASSED ] 25 tests. 82/90 Test #82: MdrunCoordinationCouplingTests1Rank ....... Passed 0.72 sec test 83 Start 83: MdrunCoordinationCouplingTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 25 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 53%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 36 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.004 0.002 195.3 83: (ns/day) (hour/ns) 83: Performance: 772.440 0.031 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 4.0%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.0%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.7 83: (ns/day) (hour/ns) 83: Performance: 1607.880 0.015 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 37%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1979.625 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1957.297 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1848.086 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.3%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1918.292 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (768 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 24 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.9 83: (ns/day) (hour/ns) 83: Performance: 1377.593 0.017 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.2%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.6%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.8 83: (ns/day) (hour/ns) 83: Performance: 1629.140 0.015 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1958.853 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.5%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1840.632 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 40%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1798.713 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 1844.489 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (176 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 53%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.0 83: (ns/day) (hour/ns) 83: Performance: 1356.810 0.018 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 4.1%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.0%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 24 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1585.943 0.015 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.7%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1895.859 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.7%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 1779.747 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 32 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1795.830 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.1 83: (ns/day) (hour/ns) 83: Performance: 1815.143 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (412 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 54%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.1 83: (ns/day) (hour/ns) 83: Performance: 1372.070 0.017 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.5%. 83: 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1605.994 0.015 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1948.938 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1785.938 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 1818.894 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1848.086 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (127 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.6 83: (ns/day) (hour/ns) 83: Performance: 1457.956 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1805.302 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 2165.030 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 2050.456 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2061.433 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2055.930 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (569 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1482.337 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.5 83: (ns/day) (hour/ns) 83: Performance: 1744.716 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 2045.350 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1957.608 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1991.464 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2042.976 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (155 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.4 83: (ns/day) (hour/ns) 83: Performance: 1351.748 0.018 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1741.264 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.1 83: (ns/day) (hour/ns) 83: Performance: 2033.535 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 1960.412 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 1956.365 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 187.7 83: (ns/day) (hour/ns) 83: Performance: 1954.813 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (533 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 25 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.2 83: (ns/day) (hour/ns) 83: Performance: 1499.840 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1683.222 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 2078.473 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 1995.334 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.4 83: (ns/day) (hour/ns) 83: Performance: 1896.151 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 1954.193 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (183 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.9 83: (ns/day) (hour/ns) 83: Performance: 1593.532 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1789.830 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 2256.215 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 2135.388 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 32 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2147.297 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 2114.136 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (92 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.0 83: (ns/day) (hour/ns) 83: Performance: 1537.074 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1774.876 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 2139.838 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2040.269 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 1999.544 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 2030.184 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (72 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.6 83: (ns/day) (hour/ns) 83: Performance: 1509.395 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1718.436 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 2016.231 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1990.177 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 2000.518 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 187.9 83: (ns/day) (hour/ns) 83: Performance: 2067.660 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (547 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1549.835 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1889.463 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 2129.115 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 2068.702 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.3 83: (ns/day) (hour/ns) 83: Performance: 2075.322 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 2070.788 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (219 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.8 83: (ns/day) (hour/ns) 83: Performance: 1589.420 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 191.8 83: (ns/day) (hour/ns) 83: Performance: 1882.534 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 2219.234 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 2160.096 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 2010.966 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 2140.582 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (79 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.7 83: (ns/day) (hour/ns) 83: Performance: 1521.322 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.3 83: (ns/day) (hour/ns) 83: Performance: 1844.765 0.013 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 2137.240 0.011 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.0 83: (ns/day) (hour/ns) 83: Performance: 1966.670 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1967.298 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1946.168 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (564 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 192.0 83: (ns/day) (hour/ns) 83: Performance: 1514.962 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.4 83: (ns/day) (hour/ns) 83: Performance: 1719.875 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 2057.303 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1999.544 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1961.036 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1974.549 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (108 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 26 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.8 83: (ns/day) (hour/ns) 83: Performance: 1542.655 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 191.1 83: (ns/day) (hour/ns) 83: Performance: 1679.093 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 2052.505 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1972.968 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.2 83: (ns/day) (hour/ns) 83: Performance: 1978.354 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1985.687 0.012 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (479 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.2 83: (ns/day) (hour/ns) 83: Performance: 1001.071 0.024 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1234.959 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1273.113 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1206.895 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.7%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.7%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1325.429 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.1%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1326.571 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (103 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.5 83: (ns/day) (hour/ns) 83: Performance: 1020.304 0.024 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 56%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.5 83: (ns/day) (hour/ns) 83: Performance: 1145.624 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.5%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.3 83: (ns/day) (hour/ns) 83: Performance: 1226.721 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.4 83: (ns/day) (hour/ns) 83: Performance: 1222.219 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.5%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.4 83: (ns/day) (hour/ns) 83: Performance: 1209.501 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1246.075 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (228 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 59%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 191.8 83: (ns/day) (hour/ns) 83: Performance: 1045.409 0.023 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.9 83: (ns/day) (hour/ns) 83: Performance: 1188.960 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.054 0.027 199.6 83: (ns/day) (hour/ns) 83: Performance: 54.172 0.443 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1192.411 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1168.439 0.021 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.5%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.003 108.7 83: (ns/day) (hour/ns) 83: Performance: 518.002 0.046 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (538 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 192.1 83: (ns/day) (hour/ns) 83: Performance: 836.526 0.029 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.0 83: (ns/day) (hour/ns) 83: Performance: 1264.100 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1402.845 0.017 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1323.436 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.0 83: (ns/day) (hour/ns) 83: Performance: 1323.436 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.2 83: (ns/day) (hour/ns) 83: Performance: 1341.739 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (134 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 191.0 83: (ns/day) (hour/ns) 83: Performance: 933.565 0.026 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.7 83: (ns/day) (hour/ns) 83: Performance: 1235.331 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.5 83: (ns/day) (hour/ns) 83: Performance: 1355.168 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1403.324 0.017 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.9 83: (ns/day) (hour/ns) 83: Performance: 1306.595 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.8 83: (ns/day) (hour/ns) 83: Performance: 1306.179 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (143 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.151 0.075 199.7 83: (ns/day) (hour/ns) 83: Performance: 19.486 1.232 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.2 83: (ns/day) (hour/ns) 83: Performance: 1243.434 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.3 83: (ns/day) (hour/ns) 83: Performance: 1339.405 0.018 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 188.6 83: (ns/day) (hour/ns) 83: Performance: 1263.712 0.019 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 188.7 83: (ns/day) (hour/ns) 83: Performance: 1099.125 0.022 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.005 0.003 145.2 83: (ns/day) (hour/ns) 83: Performance: 442.524 0.054 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (459 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.004 0.002 190.7 83: (ns/day) (hour/ns) 83: Performance: 769.065 0.031 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.2 83: (ns/day) (hour/ns) 83: Performance: 969.409 0.025 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.001 189.6 83: (ns/day) (hour/ns) 83: Performance: 1063.455 0.023 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 8 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.004 0.002 188.8 83: (ns/day) (hour/ns) 83: Performance: 705.479 0.034 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 8 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.004 0.002 189.5 83: (ns/day) (hour/ns) 83: Performance: 726.699 0.033 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.8 83: (ns/day) (hour/ns) 83: Performance: 1185.185 0.020 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (248 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 12 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.008 0.004 192.1 83: (ns/day) (hour/ns) 83: Performance: 352.952 0.068 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 18 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.005 0.003 193.8 83: (ns/day) (hour/ns) 83: Performance: 579.275 0.041 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.006 0.003 190.4 83: (ns/day) (hour/ns) 83: Performance: 437.511 0.055 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 190.8 83: (ns/day) (hour/ns) 83: Performance: 807.947 0.030 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.006 197.3 83: (ns/day) (hour/ns) 83: Performance: 236.110 0.102 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.007 0.004 189.9 83: (ns/day) (hour/ns) 83: Performance: 407.487 0.059 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (463 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.007 0.003 191.5 83: (ns/day) (hour/ns) 83: Performance: 421.641 0.057 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.006 0.003 189.2 83: (ns/day) (hour/ns) 83: Performance: 473.218 0.051 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.005 0.003 190.1 83: (ns/day) (hour/ns) 83: Performance: 539.173 0.045 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.006 0.003 189.6 83: (ns/day) (hour/ns) 83: Performance: 505.257 0.048 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.006 0.003 189.9 83: (ns/day) (hour/ns) 83: Performance: 496.082 0.048 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 21 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.007 0.004 191.9 83: (ns/day) (hour/ns) 83: Performance: 412.618 0.058 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (81 ms) 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (7494 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 25 tests from 1 test suite ran. (7505 ms total) 83: [ PASSED ] 25 tests. 83/90 Test #83: MdrunCoordinationCouplingTests2Ranks ...... Passed 7.52 sec test 84 Start 84: MdrunCoordinationConstraintsTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1761.680 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2111.962 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2429.256 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2247.572 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2299.587 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2314.273 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4485 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1761.176 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2049.432 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 1797.664 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2198.642 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2234.528 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1870.815 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1441 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1795.045 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2098.295 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2397.118 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2286.783 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2187.711 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1750.666 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1455 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1843.937 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2193.944 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.002 98.0 84: (ns/day) (hour/ns) 84: Performance: 761.225 0.032 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2322.124 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2362.191 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2077.772 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1459 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1465.412 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2147.297 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2410.248 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2302.165 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2174.583 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2244.296 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1444 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1813.540 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1731.477 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2379.526 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2238.588 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2280.857 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1874.800 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1431 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1798.713 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 2097.580 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1897.903 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2228.063 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2151.045 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 2089.045 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1440 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1727.592 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.002 98.5 84: (ns/day) (hour/ns) 84: Performance: 614.155 0.039 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2173.049 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2114.862 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1983.449 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2056.960 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1470 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1690.613 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1959.476 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 82.1 84: (ns/day) (hour/ns) 84: Performance: 1692.936 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1913.228 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2006.055 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1994.365 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1505 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1357.557 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1529.063 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1399.499 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1626.774 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1641.512 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1597.250 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1491 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.7 84: (ns/day) (hour/ns) 84: Performance: 1325.144 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1468.206 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1540.919 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1483.408 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1274.694 0.019 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1540.148 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1464 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1198.792 0.020 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1592.708 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1695.265 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1351.007 0.018 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1567.581 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1624.629 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1456 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1119.701 0.021 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1471.714 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1656.519 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1512.544 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1296.421 0.019 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1526.411 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1449 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (21998 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (22030 ms total) 84: [ PASSED ] 13 tests. 84/90 Test #84: MdrunCoordinationConstraintsTests1Rank .... Passed 22.19 sec test 85 Start 85: MdrunCoordinationConstraintsTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 13 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.4 85: (ns/day) (hour/ns) 85: Performance: 1396.010 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1652.077 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.9%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 6 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1932.735 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1837.886 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 1824.550 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1866.281 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1774 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.6 85: (ns/day) (hour/ns) 85: Performance: 1372.681 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.6 85: (ns/day) (hour/ns) 85: Performance: 1668.181 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1829.698 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1725.415 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1784.128 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1722.039 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1756 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.9 85: (ns/day) (hour/ns) 85: Performance: 1378.980 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1630.434 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1801.607 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 10 % of the run time was spent in domain decomposition, 85: 5 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1697.835 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1688.759 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 1743.976 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1995 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.4 85: (ns/day) (hour/ns) 85: Performance: 1443.438 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1728.804 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1961.973 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1824.280 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1866.281 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1733.182 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2094 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1410.554 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1682.763 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1866.847 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1800.553 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1734.646 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1801.607 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1878 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1425.074 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 1666.602 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1886.859 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1817.016 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1852.810 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1795.045 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2191 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.7 85: (ns/day) (hour/ns) 85: Performance: 1428.709 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.8 85: (ns/day) (hour/ns) 85: Performance: 1671.576 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1838.434 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1786.715 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.8 85: (ns/day) (hour/ns) 85: Performance: 1830.242 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1802.925 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1975 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.5 85: (ns/day) (hour/ns) 85: Performance: 1401.887 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.4 85: (ns/day) (hour/ns) 85: Performance: 1622.063 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1779.490 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.6 85: (ns/day) (hour/ns) 85: Performance: 1713.894 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1697.601 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1666.151 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1979 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.6 85: (ns/day) (hour/ns) 85: Performance: 1380.680 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.6 85: (ns/day) (hour/ns) 85: Performance: 1650.306 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1795.306 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1717.717 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1670.217 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1650.306 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1860 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.391 0.195 199.9 85: (ns/day) (hour/ns) 85: Performance: 7.520 3.192 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1167.996 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.382 0.191 199.9 85: (ns/day) (hour/ns) 85: Performance: 7.685 3.123 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1256.110 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1213.671 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1308.676 0.018 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2811 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 191.9 85: (ns/day) (hour/ns) 85: Performance: 953.578 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.3 85: (ns/day) (hour/ns) 85: Performance: 1200.427 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1182.342 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1120.719 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1108.918 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1137.375 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2005 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 189.3 85: (ns/day) (hour/ns) 85: Performance: 919.012 0.026 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1160.296 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1273.508 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.7 85: (ns/day) (hour/ns) 85: Performance: 1140.745 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 1198.209 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1190.568 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1727 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 189.6 85: (ns/day) (hour/ns) 85: Performance: 971.549 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.166 0.083 199.8 85: (ns/day) (hour/ns) 85: Performance: 17.629 1.361 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1218.351 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1131.630 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1147.117 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.047 199.7 85: (ns/day) (hour/ns) 85: Performance: 31.045 0.773 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2649 ms) 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (26701 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 13 tests from 1 test suite ran. (26709 ms total) 85: [ PASSED ] 13 tests. 85/90 Test #85: MdrunCoordinationConstraintsTests2Ranks ... Passed 26.73 sec test 86 Start 86: MdrunFEPTests 86: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 14 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 2 tests from ExpandedEnsembleTest 86: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 16 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.150 0.075 199.9 86: (ns/day) (hour/ns) 86: Performance: 19.531 1.229 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.007 197.5 86: (ns/day) (hour/ns) 86: Performance: 107.512 0.223 86: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (118 ms) 86: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 1 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.003 0.002 195.7 86: (ns/day) (hour/ns) 86: Performance: 101.183 0.237 86: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (17 ms) 86: [----------] 2 tests from ExpandedEnsembleTest (136 ms total) 86: 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -307370257 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.078 0.039 199.7 86: (ns/day) (hour/ns) 86: Performance: 46.487 0.516 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 86: 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (139 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -12584057 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.896 0.448 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.048 5.929 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (550 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -134774785 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.022 199.5 86: (ns/day) (hour/ns) 86: Performance: 80.690 0.297 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (107 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 155]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 155]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to 1002430460 86: 86: Generated 171 of the 171 non-bonded parameter combinations 86: 86: Generated 171 of the 171 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 358.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 1 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.075 0.037 199.7 86: (ns/day) (hour/ns) 86: Performance: 48.541 0.494 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (59 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 165]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 165]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to -536940837 86: 86: Generated 190 of the 190 non-bonded parameter combinations 86: 86: Generated 190 of the 190 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'CL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'CL' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 361.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 2 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.058 0.029 199.7 86: (ns/day) (hour/ns) 86: Performance: 62.055 0.387 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (46 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 86: and vdw_modifier=Force-switch 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 100 steps, 0.1 ps. 86: Setting the LD random seed to -168035329 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.329 0.165 199.9 86: (ns/day) (hour/ns) 86: Performance: 52.955 0.453 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (252 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There were 11 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -5243213 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.114 0.057 199.8 86: (ns/day) (hour/ns) 86: Performance: 31.675 0.758 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (144 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: Removing center of mass motion in the presence of position restraints 86: might cause artifacts. When you are using position restraints to 86: equilibrate a macro-molecule, the artifacts are usually negligible. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 11 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -536936513 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.109 0.055 199.8 86: (ns/day) (hour/ns) 86: Performance: 33.239 0.722 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (135 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -314673322 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.87 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.036 0.018 199.2 86: (ns/day) (hour/ns) 86: Performance: 99.505 0.241 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (97 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.044 0.022 199.2 86: (ns/day) (hour/ns) 86: Performance: 82.162 0.292 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: Setting the LD random seed to -343932951 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.87 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (104 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to 2069879780 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.93 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.089 0.044 199.8 86: (ns/day) (hour/ns) 86: Performance: 40.787 0.588 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (126 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -77766785 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.88 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.023 199.4 86: (ns/day) (hour/ns) 86: Performance: 80.223 0.299 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (98 ms) 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (1867 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 14 tests from 2 test suites ran. (2018 ms total) 86: [ PASSED ] 14 tests. 86/90 Test #86: MdrunFEPTests ............................. Passed 2.03 sec test 87 Start 87: MdrunPullTests 87: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 4 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from PullTest/PullIntegrationTest 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.600 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.014 199.3 87: (ns/day) (hour/ns) 87: Performance: 126.741 0.189 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (271 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.301 nm 0.400 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.030 0.015 199.3 87: (ns/day) (hour/ns) 87: Performance: 118.838 0.202 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (304 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Pull group 3 'r_3' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1292.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.357 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.500 nm 87: 1 3 2 87: 3 3 8 0.331 nm 0.400 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 199.6 87: (ns/day) (hour/ns) 87: Performance: 73.314 0.327 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (317 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.000 nm 87: 1 3 2 87: 2 3 5 0.050 nm 0.000 nm 87: 87: There was 1 NOTE 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 199.5 87: (ns/day) (hour/ns) 87: Performance: 73.844 0.325 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (319 ms) 87: [----------] 4 tests from PullTest/PullIntegrationTest (1213 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 4 tests from 1 test suite ran. (1224 ms total) 87: [ PASSED ] 4 tests. 87/90 Test #87: MdrunPullTests ............................ Passed 1.24 sec test 88 Start 88: MdrunRotationTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 12 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 12 tests from RotationWorks/RotationTest 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 88: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: trr version: GMX_trn_file (single precision) 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -237256833 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: NOTE: 16 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.141 0.071 199.8 88: (ns/day) (hour/ns) 88: Performance: 63.458 0.378 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (79 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 88: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1082264065 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 191.7 88: (ns/day) (hour/ns) 88: Performance: 5095.773 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (8 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 88: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1038741374 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 192.2 88: (ns/day) (hour/ns) 88: Performance: 5228.682 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (5 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 88: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -872416065 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 191.6 88: (ns/day) (hour/ns) 88: Performance: 5027.793 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (10 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 88: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -269000981 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 191.2 88: (ns/day) (hour/ns) 88: Performance: 4841.770 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (11 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 88: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2128608955 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.011 0.005 197.6 88: (ns/day) (hour/ns) 88: Performance: 838.077 0.029 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (10 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 88: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -17597514 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: NOTE: 18 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.130 0.065 199.9 88: (ns/day) (hour/ns) 88: Performance: 69.099 0.347 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (72 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 88: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2147090351 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.001 192.5 88: (ns/day) (hour/ns) 88: Performance: 5291.819 0.005 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (10 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 88: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1601666031 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.015 0.007 198.1 88: (ns/day) (hour/ns) 88: Performance: 611.446 0.039 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (12 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 88: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -2118145 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.009 0.005 197.2 88: (ns/day) (hour/ns) 88: Performance: 985.522 0.024 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (9 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 88: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -631109 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.004 0.002 196.2 88: (ns/day) (hour/ns) 88: Performance: 2313.019 0.010 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (6 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 88: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -8986641 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.003 0.002 195.8 88: (ns/day) (hour/ns) 88: Performance: 2583.871 0.009 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (6 ms) 88: [----------] 12 tests from RotationWorks/RotationTest (247 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 12 tests from 1 test suite ran. (254 ms total) 88: [ PASSED ] 12 tests. 88/90 Test #88: MdrunRotationTests ........................ Passed 0.27 sec test 89 Start 89: MdrunSimulatorComparison 89: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 94 tests from 4 test suites. 89: [----------] Global test environment set-up. 89: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 199.2 89: (ns/day) (hour/ns) 89: Performance: 185.131 0.130 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.8 89: (ns/day) (hour/ns) 89: Performance: 1724.208 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 89: 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (16 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 195.1 89: (ns/day) (hour/ns) 89: Performance: 1464.019 0.016 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.4 89: (ns/day) (hour/ns) 89: Performance: 1731.477 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.3 89: (ns/day) (hour/ns) 89: Performance: 1618.653 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.1 89: (ns/day) (hour/ns) 89: Performance: 1657.410 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (14 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.013 0.007 198.7 89: (ns/day) (hour/ns) 89: Performance: 217.781 0.110 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.3 89: (ns/day) (hour/ns) 89: Performance: 1723.725 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (13 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.0 89: (ns/day) (hour/ns) 89: Performance: 1292.342 0.019 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.8 89: (ns/day) (hour/ns) 89: Performance: 1662.778 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (10 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.8 89: (ns/day) (hour/ns) 89: Performance: 1584.107 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 32 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.022 0.011 199.2 89: (ns/day) (hour/ns) 89: Performance: 134.502 0.178 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (23 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There were 2 WARNINGs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 197.9 89: (ns/day) (hour/ns) 89: Performance: 359.953 0.067 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.7 89: (ns/day) (hour/ns) 89: Performance: 1708.429 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (20 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.1 89: (ns/day) (hour/ns) 89: Performance: 1433.029 0.017 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.3 89: (ns/day) (hour/ns) 89: Performance: 1674.074 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (10 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: MTTK coupling is deprecated and will soon be removed 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.7 89: (ns/day) (hour/ns) 89: Performance: 183.209 0.131 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.1 89: (ns/day) (hour/ns) 89: Performance: 1483.765 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (14 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.3 89: (ns/day) (hour/ns) 89: Performance: 286.726 0.084 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.3 89: (ns/day) (hour/ns) 89: Performance: 1654.295 0.015 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (11 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.3 89: (ns/day) (hour/ns) 89: Performance: 285.543 0.084 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.1 89: (ns/day) (hour/ns) 89: Performance: 1571.981 0.015 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (12 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: MTTK coupling is deprecated and will soon be removed 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 194.7 89: (ns/day) (hour/ns) 89: Performance: 925.431 0.026 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.9 89: (ns/day) (hour/ns) 89: Performance: 1447.508 0.017 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (18 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.6 89: (ns/day) (hour/ns) 89: Performance: 1583.700 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.3 89: (ns/day) (hour/ns) 89: Performance: 1474.532 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.1 89: (ns/day) (hour/ns) 89: Performance: 1522.638 0.016 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.015 0.008 198.3 89: (ns/day) (hour/ns) 89: Performance: 189.330 0.127 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (14 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.2 89: (ns/day) (hour/ns) 89: Performance: 1493.477 0.016 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.6 89: (ns/day) (hour/ns) 89: Performance: 1678.636 0.014 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.9 89: (ns/day) (hour/ns) 89: Performance: 1363.567 0.018 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.0 89: (ns/day) (hour/ns) 89: Performance: 1575.599 0.015 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.2 89: (ns/day) (hour/ns) 89: Performance: 1381.299 0.017 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.1 89: (ns/day) (hour/ns) 89: Performance: 1517.388 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.9 89: (ns/day) (hour/ns) 89: Performance: 1415.578 0.017 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 194.5 89: (ns/day) (hour/ns) 89: Performance: 1082.325 0.022 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 199.2 89: (ns/day) (hour/ns) 89: Performance: 183.051 0.131 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.7 89: (ns/day) (hour/ns) 89: Performance: 1488.426 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (312 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 199.0 89: (ns/day) (hour/ns) 89: Performance: 180.663 0.133 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.006 0.003 196.0 89: (ns/day) (hour/ns) 89: Performance: 455.093 0.053 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (303 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.1 89: (ns/day) (hour/ns) 89: Performance: 298.942 0.080 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 197.5 89: (ns/day) (hour/ns) 89: Performance: 379.160 0.063 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (307 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.8 89: (ns/day) (hour/ns) 89: Performance: 181.130 0.133 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 197.8 89: (ns/day) (hour/ns) 89: Performance: 345.073 0.070 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (309 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.8 89: (ns/day) (hour/ns) 89: Performance: 1167.000 0.021 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 197.7 89: (ns/day) (hour/ns) 89: Performance: 344.899 0.070 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (302 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.8 89: (ns/day) (hour/ns) 89: Performance: 181.141 0.132 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.8 89: (ns/day) (hour/ns) 89: Performance: 1515.148 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (312 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There were 2 WARNINGs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.8 89: (ns/day) (hour/ns) 89: Performance: 180.716 0.133 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.009 0.004 197.9 89: (ns/day) (hour/ns) 89: Performance: 329.056 0.073 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (309 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.0 89: (ns/day) (hour/ns) 89: Performance: 1203.006 0.020 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.009 0.004 197.8 89: (ns/day) (hour/ns) 89: Performance: 337.900 0.071 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (318 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.8 89: (ns/day) (hour/ns) 89: Performance: 180.986 0.133 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 192.2 89: (ns/day) (hour/ns) 89: Performance: 1095.801 0.022 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (307 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.013 0.006 198.3 89: (ns/day) (hour/ns) 89: Performance: 232.151 0.103 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.012 0.006 197.8 89: (ns/day) (hour/ns) 89: Performance: 236.655 0.101 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (303 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.015 0.007 198.7 89: (ns/day) (hour/ns) 89: Performance: 200.710 0.120 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.4 89: (ns/day) (hour/ns) 89: Performance: 1479.845 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (308 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.005 0.002 196.2 89: (ns/day) (hour/ns) 89: Performance: 603.093 0.040 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.005 0.003 195.9 89: (ns/day) (hour/ns) 89: Performance: 571.060 0.042 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (298 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.1 89: (ns/day) (hour/ns) 89: Performance: 292.401 0.082 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.3 89: (ns/day) (hour/ns) 89: Performance: 186.538 0.129 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (292 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 89: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (4218 ms total) 89: 89: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.4 89: (ns/day) (hour/ns) 89: Performance: 1268.134 0.019 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 198.5 89: (ns/day) (hour/ns) 89: Performance: 354.689 0.068 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (20 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 190.9 89: (ns/day) (hour/ns) 89: Performance: 1989.213 0.012 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 195.2 89: (ns/day) (hour/ns) 89: Performance: 1428.047 0.017 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.4 89: (ns/day) (hour/ns) 89: Performance: 1727.108 0.014 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.9 89: (ns/day) (hour/ns) 89: Performance: 1357.557 0.018 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (13 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 191.3 89: (ns/day) (hour/ns) 89: Performance: 2124.343 0.011 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.4 89: (ns/day) (hour/ns) 89: Performance: 1561.621 0.015 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 190.3 89: (ns/day) (hour/ns) 89: Performance: 1873.660 0.013 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.3 89: (ns/day) (hour/ns) 89: Performance: 1482.694 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (9 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.2 89: (ns/day) (hour/ns) 89: Performance: 1235.826 0.019 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.2 89: (ns/day) (hour/ns) 89: Performance: 1440.064 0.017 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (13 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.015 0.007 198.4 89: (ns/day) (hour/ns) 89: Performance: 196.429 0.122 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.3 89: (ns/day) (hour/ns) 89: Performance: 1456.750 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (14 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.8 89: (ns/day) (hour/ns) 89: Performance: 1385.960 0.017 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.5 89: (ns/day) (hour/ns) 89: Performance: 1600.570 0.015 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.7 89: (ns/day) (hour/ns) 89: Performance: 1376.054 0.017 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.0 89: (ns/day) (hour/ns) 89: Performance: 1510.690 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There were 2 WARNINGs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 194.2 89: (ns/day) (hour/ns) 89: Performance: 941.699 0.025 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.6 89: (ns/day) (hour/ns) 89: Performance: 1438.719 0.017 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (14 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 191.0 89: (ns/day) (hour/ns) 89: Performance: 2033.870 0.012 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.2 89: (ns/day) (hour/ns) 89: Performance: 1409.102 0.017 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (7 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.013 0.006 197.9 89: (ns/day) (hour/ns) 89: Performance: 228.704 0.105 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.6 89: (ns/day) (hour/ns) 89: Performance: 1538.994 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (13 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.6 89: (ns/day) (hour/ns) 89: Performance: 1361.156 0.018 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.8 89: (ns/day) (hour/ns) 89: Performance: 1478.070 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.2 89: (ns/day) (hour/ns) 89: Performance: 1347.756 0.018 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.1 89: (ns/day) (hour/ns) 89: Performance: 1517.014 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (8 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 193.6 89: (ns/day) (hour/ns) 89: Performance: 1184.502 0.020 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.122 0.061 199.9 89: (ns/day) (hour/ns) 89: Performance: 24.082 0.997 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (72 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 13 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.135 0.067 199.8 89: (ns/day) (hour/ns) 89: Performance: 21.801 1.101 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 13 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.149 0.074 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.747 1.215 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (427 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 13 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.135 0.067 199.9 89: (ns/day) (hour/ns) 89: Performance: 21.814 1.100 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 12 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.148 0.074 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.834 1.210 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (438 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 12 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.138 0.069 199.8 89: (ns/day) (hour/ns) 89: Performance: 21.272 1.128 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 12 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.150 0.075 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.566 1.227 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (435 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.127 0.063 199.8 89: (ns/day) (hour/ns) 89: Performance: 23.190 1.035 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.139 0.069 199.9 89: (ns/day) (hour/ns) 89: Performance: 21.181 1.133 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (424 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.127 0.063 199.8 89: (ns/day) (hour/ns) 89: Performance: 23.158 1.036 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.138 0.069 199.9 89: (ns/day) (hour/ns) 89: Performance: 21.268 1.128 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (427 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.131 0.066 199.8 89: (ns/day) (hour/ns) 89: Performance: 22.420 1.070 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.143 0.071 199.9 89: (ns/day) (hour/ns) 89: Performance: 20.556 1.168 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (428 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.130 0.065 199.8 89: (ns/day) (hour/ns) 89: Performance: 22.556 1.064 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.142 0.071 199.9 89: (ns/day) (hour/ns) 89: Performance: 20.669 1.161 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (426 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.127 0.063 199.8 89: (ns/day) (hour/ns) 89: Performance: 23.133 1.037 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.135 0.067 199.9 89: (ns/day) (hour/ns) 89: Performance: 21.788 1.102 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (423 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.127 0.064 199.8 89: (ns/day) (hour/ns) 89: Performance: 23.110 1.038 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.147 0.074 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.972 1.202 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (423 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There were 2 WARNINGs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.105 0.053 199.7 89: (ns/day) (hour/ns) 89: Performance: 27.907 0.860 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.009 0.004 198.1 89: (ns/day) (hour/ns) 89: Performance: 333.113 0.072 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (347 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.1 89: (ns/day) (hour/ns) 89: Performance: 1595.182 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.009 0.005 198.1 89: (ns/day) (hour/ns) 89: Performance: 312.024 0.077 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (309 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 196.8 89: (ns/day) (hour/ns) 89: Performance: 377.649 0.064 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.016 0.008 198.9 89: (ns/day) (hour/ns) 89: Performance: 185.846 0.129 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (312 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.2 89: (ns/day) (hour/ns) 89: Performance: 1598.079 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.005 0.003 196.6 89: (ns/day) (hour/ns) 89: Performance: 557.924 0.043 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (304 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.015 0.007 198.1 89: (ns/day) (hour/ns) 89: Performance: 196.755 0.122 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.009 0.005 198.0 89: (ns/day) (hour/ns) 89: Performance: 313.980 0.076 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (301 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.2 89: (ns/day) (hour/ns) 89: Performance: 1605.157 0.015 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.008 0.004 197.9 89: (ns/day) (hour/ns) 89: Performance: 346.334 0.069 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (304 ms) 89: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (5966 ms total) 89: 89: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'FirstWaterMolecule' has 3 atoms 89: Pull group 2 'SecondWaterMolecule' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 9.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 2573.591 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 1.112 nm 1.000 nm 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 3 of the 3 non-bonded parameter combinations 89: 89: Generated 3 of the 3 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.2 89: (ns/day) (hour/ns) 89: Performance: 293.823 0.082 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.7 89: (ns/day) (hour/ns) 89: Performance: 1484.123 0.016 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (15 ms) 89: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (15 ms total) 89: 89: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'FirstWaterMolecule' has 3 atoms 89: Pull group 2 'SecondWaterMolecule' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 9.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 2573.591 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 1.112 nm 1.000 nm 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 3 of the 3 non-bonded parameter combinations 89: 89: Generated 3 of the 3 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.013 0.007 197.7 89: (ns/day) (hour/ns) 89: Performance: 225.193 0.107 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 194.6 89: (ns/day) (hour/ns) 89: Performance: 1330.294 0.018 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (17 ms) 89: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (17 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 94 tests from 4 test suites ran. (10248 ms total) 89: [ PASSED ] 94 tests. 89/90 Test #89: MdrunSimulatorComparison .................. Passed 10.26 sec test 90 Start 90: MdrunVirtualSiteTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 37 tests from 2 test suites. 90: [----------] Global test environment set-up. 90: [----------] 1 test from VirtualSiteVelocityTest 90: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 90: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 90: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 90: 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.8%. 90: The balanceable part of the MD step is 41%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.3%. 90: 90: 90: NOTE: 38 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.003 0.002 194.1 90: (ns/day) (hour/ns) 90: Performance: 471.314 0.051 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: trr version: GMX_trn_file (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (89 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 3.3%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 1.2%. 90: 90: 90: NOTE: 33 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 191.5 90: (ns/day) (hour/ns) 90: Performance: 658.156 0.036 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (26 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.3%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.9%. 90: 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.8 90: (ns/day) (hour/ns) 90: Performance: 905.341 0.027 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (23 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 31 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.4 90: (ns/day) (hour/ns) 90: Performance: 914.351 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (38 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.7 90: (ns/day) (hour/ns) 90: Performance: 973.289 0.025 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (109 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.0 90: (ns/day) (hour/ns) 90: Performance: 984.452 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (289 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 188.6 90: (ns/day) (hour/ns) 90: Performance: 1023.855 0.023 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (42 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 187.8 90: (ns/day) (hour/ns) 90: Performance: 986.239 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (16 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 31 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.1 90: (ns/day) (hour/ns) 90: Performance: 917.180 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (20 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.3%. 90: The balanceable part of the MD step is 39%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.9%. 90: 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.9 90: (ns/day) (hour/ns) 90: Performance: 878.161 0.027 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (22 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.2%. 90: The balanceable part of the MD step is 42%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.5%. 90: 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.4 90: (ns/day) (hour/ns) 90: Performance: 862.486 0.028 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (27 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.001 0.001 189.5 90: (ns/day) (hour/ns) 90: Performance: 991.636 0.024 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (33 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.5 90: (ns/day) (hour/ns) 90: Performance: 931.322 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (23 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.6 90: (ns/day) (hour/ns) 90: Performance: 907.356 0.026 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (15 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 27 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 188.9 90: (ns/day) (hour/ns) 90: Performance: 854.800 0.028 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (30 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 29 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 190.2 90: (ns/day) (hour/ns) 90: Performance: 976.640 0.025 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (21 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 189.6 90: (ns/day) (hour/ns) 90: Performance: 948.108 0.025 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (16 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 36 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 191.6 90: (ns/day) (hour/ns) 90: Performance: 596.414 0.040 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (33 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 190.6 90: (ns/day) (hour/ns) 90: Performance: 878.279 0.027 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (529 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 33 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 190.9 90: (ns/day) (hour/ns) 90: Performance: 685.043 0.035 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (31 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 28 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.003 0.001 193.1 90: (ns/day) (hour/ns) 90: Performance: 550.788 0.044 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (40 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1483 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 37 tests from 2 test suites ran. (1490 ms total) 90: [ PASSED ] 37 tests. 90/90 Test #90: MdrunVirtualSiteTests ..................... Passed 1.50 sec 100% tests passed, 0 tests failed out of 90 Label Time Summary: GTest = 256.13 sec*proc (88 tests) IntegrationTest = 144.19 sec*proc (28 tests) MpiTest = 181.95 sec*proc (21 tests) QuickGpuTest = 46.66 sec*proc (22 tests) SlowGpuTest = 189.26 sec*proc (14 tests) SlowTest = 105.47 sec*proc (14 tests) UnitTest = 6.48 sec*proc (46 tests) Total Test time (real) = 129.44 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib /usr/bin/make -j12 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target thread_mpi /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/usergpuids.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 14%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi.so.10 -o ../../lib/libgromacs_mpi.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi.so.10.0.0 ../../lib/libgromacs_mpi.so.10 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi.so.0 -o ../../lib/libgmxapi_mpi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi.so.0.4.0 ../../lib/libgmxapi_mpi.so.0 ../../lib/libgmxapi_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -MF CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o.d -o CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/sessionresources.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/launch_0_2_1.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/module.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_tprfile.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_resources.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_resources.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_resources.a CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_resources.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_ensemblepotential.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_ensemblepotential.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_ensemblepotential.a CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_ensemblepotential.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/nullpotential.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_gromacs_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_test.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_test /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/mpicxx -DGMX_DOUBLE=0 -Dgmxapi_extension_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -MF CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o.d -o CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file=CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-313-aarch64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o ../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/strip /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/gmxapi_staging/gmxapi/_gmxapi.cpython-313-aarch64-linux-gnu.so /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file=CMakeFiles/gmxapi_extension.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../lib/myplugin.cpython-313-aarch64-linux-gnu.so CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o ../../../../lib/libgmxapi_extension_ensemblepotential.a ../../../../lib/libgmxapi_extension_test.a ../../../../lib/libgmxapi_extension_resources.a ../../../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/strip /build/reproducible-path/gromacs-2025.0/build/mpi/lib/myplugin.cpython-313-aarch64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target gmxapi_extension [ 98%] Built target _gmxapi cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -j12 -C build/mpi-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target thread_mpi /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/forceelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 4%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi_d.so.10 -o ../../lib/libgromacs_mpi_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.10.0.0 ../../lib/libgromacs_mpi_d.so.10 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi_d ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi_d.so.0 -o ../../lib/libgmxapi_mpi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi_d.so.0.4.0 ../../lib/libgmxapi_mpi_d.so.0 ../../lib/libgmxapi_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib /usr/bin/make -j12 -C build/mpi tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 76 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 1%] Built target gmx_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 1%] Built target scanner make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 1%] Built target release-version-info make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 1%] Built target internal_rpc_xdr [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" [ 1%] Built target lmfit_objlib [ 2%] Built target tng_io_obj /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build [ 3%] Built target linearalgebra make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest-all.cc /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 5%] Built target options make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 5%] Built target mdrun_objlib [ 5%] Built target energyanalysis make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 7%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 9%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 9%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 61%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 61%] Built target gmx /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend [ 63%] Built target nblib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend [ 64%] Built target gmxapi /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.top /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target argon-forces-integration [ 64%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend [ 64%] Built target methane-water-integration make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gmxapi_extension_ensemblepotential Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Setting the LD random seed to -67114115 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' Analysing residue names: There are: 2 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gmxapi_extension_spc2_water_box cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gtest /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest_main.cc /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest_main.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest_main.so.1.13.0 -o ../../../../lib/libgtest_main.so.1.13.0 CMakeFiles/gtest_main.dir/src/gtest_main.cc.o ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 65%] Built target gtest_main /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -MF CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o.d -o CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests/test_bounding_restraint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests/test_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_histogram-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi_extension_histogram-test.dir/link.d "CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o" -o ../../../bin/gmxapi_extension_histogram-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 65%] Built target gmxapi_extension_histogram-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_bounding-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi_extension_bounding-test.dir/link.d "CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o" -o ../../../bin/gmxapi_extension_bounding-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 65%] Built target gmxapi_extension_bounding-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 65%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/interactivetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/loggertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpi_printer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/mpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stdiohelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/stringtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfilemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testfileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_device.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/test_hardware_environment.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/testoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/textblockmatchers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o -MF CMakeFiles/testutils.dir/topologyhelpers.cpp.o.d -o CMakeFiles/testutils.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tprfilegenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o -MF CMakeFiles/testutils.dir/trajectoryreader.cpp.o.d -o CMakeFiles/testutils.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/xvgtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/testutils -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/topologyhelpers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/depend /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/testsystems.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energyreader.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvars.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/interactivetest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/mpitest.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calcvir.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 69%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 71%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 71%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/xvgtest_tests.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 72%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmebsplinetest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 72%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target testutils-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target domdec-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/devicetransfers.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/extensions.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target fft-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target mdrunutility-test-shared cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/coordinatetransformation.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target nbnxm-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target listed_forces-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfit.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpwritercontext.cpp [ 75%] Built target awh-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 76%] Built target mdspan-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 76%] Built target hardware-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 76%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoption.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 76%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 76%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmetestcommon.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 77%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 77%] Built target mdtypes-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 77%] Built target taskassignment-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp [ 77%] Built target ewald-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 78%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 78%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 78%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genion.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target random-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/repeatingsection.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target topology-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/datatest.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/builder.cpp /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/timeunitmanager.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target correlations-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_vector_operations.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 82%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 84%] Built target simd-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 85%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 86%] Built target mdlib-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectionoption.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 86%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 89%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freezegroups.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisim.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 89%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 [ 89%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 89%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 90%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 90%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" [ 90%] Built target mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull_rotation.cpp [ 90%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulator.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-mpi-pme-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-mpi-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/integrator.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 93%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 93%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 93%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target workflow-details-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-mpi-test.dir/link.d "CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/traits.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-integrator-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 [ 96%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbnxmsetup.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-mpi-test.dir/link.d "CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/transformations.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib \ OMPI_MCA_rmaps_base_oversubscribe=1 \ PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -134258754 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.002 0.001 192.6 1: (ns/day) (hour/ns) 1: Performance: 424.419 0.057 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (277 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1078985420 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.001 0.001 187.8 1: (ns/day) (hour/ns) 1: Performance: 879.241 0.027 1: [ OK ] GmxApiTest.RunnerBasicMD (269 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -86982759 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.189 0.095 199.9 1: (ns/day) (hour/ns) 1: Performance: 37.474 0.640 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.170 0.085 199.9 1: (ns/day) (hour/ns) 1: Performance: 41.715 0.575 1: [ OK ] GmxApiTest.RunnerReinitialize (407 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -104866341 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 17 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.035 0.017 199.4 1: (ns/day) (hour/ns) 1: Performance: 29.032 0.827 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 34 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.040 0.020 199.6 1: (ns/day) (hour/ns) 1: Performance: 25.324 0.948 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (264 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -537657515 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 35 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.069 0.035 199.7 1: (ns/day) (hour/ns) 1: Performance: 24.380 0.984 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 31 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.031 0.016 199.4 1: (ns/day) (hour/ns) 1: Performance: 21.531 1.115 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (278 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -127426842 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (182 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1680 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1687 ms total) 1: [ PASSED ] 9 tests. 1/94 Test #1: GmxapiExternalInterfaceTests ................. Passed 1.91 sec test 2 Start 2: GmxapiMpiTests 2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests 2: Test timeout computed to be: 600 2: [==========] Running 13 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 13 tests from GmxApiTest 2: [ RUN ] GmxApiTest.AllContext 2: [ OK ] GmxApiTest.AllContext (47 ms) 2: [ RUN ] GmxApiTest.NullContext 2: [ OK ] GmxApiTest.NullContext (0 ms) 2: [ RUN ] GmxApiTest.MpiWorldContext 2: [ OK ] GmxApiTest.MpiWorldContext (40 ms) 2: [ RUN ] GmxApiTest.MpiSplitContext 2: Setting the LD random seed to -1677766679 2: [ OK ] GmxApiTest.MpiSplitContext (32 ms) 2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 2: Setting the LD random seed to -1040207957 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 26 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.096 0.024 398.8 2: (ns/day) (hour/ns) 2: Performance: 21.008 1.142 2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (540 ms) 2: [ RUN ] GmxApiTest.RunnerBasicMD 2: Setting the LD random seed to -1078013481 2: Setting the LD random seed to -16777734 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 24 % of the run time was spent in domain decomposition, 2: 5 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 10 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.185 0.046 399.4 2: (ns/day) (hour/ns) 2: Performance: 10.936 2.195 2: [ OK ] GmxApiTest.RunnerBasicMD (354 ms) 2: [ RUN ] GmxApiTest.RunnerReinitialize 2: Setting the LD random seed to -1115174 2: Setting the LD random seed to -824969748 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: Writing final coordinates. 2: 2: Core t (s) Wall t (s) (%) 2: Time: 1.160 0.290 399.9 2: (ns/day) (hour/ns) 2: Performance: 12.219 1.964 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 14 % of the run time was spent in domain decomposition, 2: 2 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.490 0.123 399.7 2: (ns/day) (hour/ns) 2: Performance: 28.881 0.831 2: [ OK ] GmxApiTest.RunnerReinitialize (800 ms) 2: [ RUN ] GmxApiTest.RunnerChainedMD 2: Setting the LD random seed to -35654722 2: Setting the LD random seed to 2137915119 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 25 % of the run time was spent in domain decomposition, 2: 14 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 6 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.145 0.036 399.3 2: (ns/day) (hour/ns) 2: Performance: 13.951 1.720 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Setting nsteps to 4 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Setting nsteps to 4 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 2: 2: Writing final coordinates. 2: 2: NOTE: 31 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.091 0.023 398.9 2: (ns/day) (hour/ns) 2: Performance: 22.250 1.079 2: 2: 2: [ OK ] GmxApiTest.RunnerChainedMD (273 ms) 2: [ RUN ] GmxApiTest.Status 2: [ OK ] GmxApiTest.Status (0 ms) 2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 2: Setting the LD random seed to -1560283273 2: Setting the LD random seed to -34742787 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 19.6%. 2: The balanceable part of the MD step is 10%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 1.9%. 2: 2: 2: NOTE: 51 % of the run time was spent in domain decomposition, 2: 25 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.439 0.110 399.7 2: (ns/day) (hour/ns) 2: Performance: 7.680 3.125 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 20.1%. 2: The balanceable part of the MD step is 11%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 2.2%. 2: 2: 2: NOTE: 48 % of the run time was spent in domain decomposition, 2: 25 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.165 0.041 399.4 2: (ns/day) (hour/ns) 2: Performance: 8.147 2.946 2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (373 ms) 2: [ RUN ] GmxApiTest.SystemConstruction 2: Setting the LD random seed to 2108939246 2: Setting the LD random seed to -1948451218 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: [ OK ] GmxApiTest.SystemConstruction (176 ms) 2: [ RUN ] GmxApiTest.SaneVersionComparisons 2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 2: [ RUN ] GmxApiTest.VersionNamed0_1_Features 2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 2: [----------] 13 tests from GmxApiTest (2679 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 13 tests from 1 test suite ran. (2759 ms total) 2: [ PASSED ] 13 tests. 2/94 Test #2: GmxapiMpiTests ............................... Passed 3.63 sec test 3 Start 3: GmxapiInternalInterfaceTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests 3: Test timeout computed to be: 600 3: [==========] Running 2 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 2 tests from GmxApiTest 3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 1567554027 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (163 ms) 3: [ RUN ] GmxApiTest.CreateApiWorkflow 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 1811907415 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.CreateApiWorkflow (148 ms) 3: [----------] 2 tests from GmxApiTest (311 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 2 tests from 1 test suite ran. (315 ms total) 3: [ PASSED ] 2 tests. 3/94 Test #3: GmxapiInternalInterfaceTests ................. Passed 0.53 sec test 4 Start 4: GmxapiInternalsMpiTests 4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests 4: Test timeout computed to be: 600 4: [==========] Running 2 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from GmxApiTest 4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 4: Setting the LD random seed to -269029381 4: Setting the LD random seed to -272655913 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (183 ms) 4: [ RUN ] GmxApiTest.CreateApiWorkflow 4: Setting the LD random seed to 2035538999 4: Setting the LD random seed to 1836318383 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: [ OK ] GmxApiTest.CreateApiWorkflow (162 ms) 4: [----------] 2 tests from GmxApiTest (346 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test suite ran. (352 ms total) 4: [ PASSED ] 2 tests. 4/94 Test #4: GmxapiInternalsMpiTests ...................... Passed 0.68 sec test 5 Start 5: NbLibListedForcesTests 5: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests 5: Test timeout computed to be: 600 5: [==========] Running 44 tests from 22 test suites. 5: [----------] Global test environment set-up. 5: [----------] 8 tests from NBlibTest 5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 5: [ RUN ] NBlibTest.BondTypesLessThanWorks 5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 5: [ RUN ] NBlibTest.CanSplitListedWork 5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 5: [ RUN ] NBlibTest.ListedForceBuffer 5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 5: [ RUN ] NBlibTest.EndToEndListedComparison 5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 5: [ RUN ] NBlibTest.shiftForcesAreCorrect 5: [ OK ] NBlibTest.shiftForcesAreCorrect (12 ms) 5: [----------] 8 tests from NBlibTest (12 ms total) 5: 5: [----------] 1 test from Kernels 5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 5: [----------] 1 test from Kernels (0 ms total) 5: 5: [----------] 1 test from FourCenter 5: [ RUN ] FourCenter.ListedForcesProperDihedralTest 5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 5: [----------] 1 test from FourCenter (0 ms total) 5: 5: [----------] 7 tests from ThreeCenter 5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 5: [----------] 7 tests from ThreeCenter (0 ms total) 5: 5: [----------] 5 tests from TwoCenter 5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesG96BondTest 5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesCubicBondTest 5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesMorseBondTest 5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesFeneBondTest 5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 5: [----------] 5 tests from TwoCenter (0 ms total) 5: 5: [----------] 5 tests from ListedExampleData 5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceForces 5: [ OK ] ListedExampleData.CanReduceForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceEnergies 5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 5: [----------] 5 tests from ListedExampleData (0 ms total) 5: 5: [----------] 1 test from LinearChainDataFixture 5: [ RUN ] LinearChainDataFixture.Multithreading 5: [ OK ] LinearChainDataFixture.Multithreading (28 ms) 5: [----------] 1 test from LinearChainDataFixture (28 ms total) 5: 5: [----------] 2 tests from ListedShims 5: [ RUN ] ListedShims.ParameterConversion 5: [ OK ] ListedShims.ParameterConversion (0 ms) 5: [ RUN ] ListedShims.GmxToNblibConversion 5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 5: [----------] 2 tests from ListedShims (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 5: 5: [----------] 1 test from ListedTransformations 5: [ RUN ] ListedTransformations.SortInteractionIndices 5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 5: [----------] 1 test from ListedTransformations (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 44 tests from 22 test suites ran. (42 ms total) 5: [ PASSED ] 44 tests. 5/94 Test #5: NbLibListedForcesTests ....................... Passed 0.30 sec test 6 Start 6: NbLibSamplesTestArgon 6: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/argon-forces-integration 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples 6: Test timeout computed to be: 1500 6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 6/94 Test #6: NbLibSamplesTestArgon ........................ Passed 0.07 sec test 7 Start 7: NbLibSamplesTestMethaneWater 7: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/methane-water-integration 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples 7: Test timeout computed to be: 1500 7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 7: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 7/94 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.10 sec test 8 Start 8: NbLibUtilTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests 8: Test timeout computed to be: 30 8: [==========] Running 16 tests from 2 test suites. 8: [----------] Global test environment set-up. 8: [----------] 6 tests from NBlibTest 8: [ RUN ] NBlibTest.isRealValued 8: [ OK ] NBlibTest.isRealValued (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasNan 8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasInf 8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 8: [ RUN ] NBlibTest.generateVelocitySize 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocitySize (0 ms) 8: [ RUN ] NBlibTest.generateVelocityCheckNumbers 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 8: [----------] 6 tests from NBlibTest (0 ms total) 8: 8: [----------] 10 tests from NblibTraitsUtils 8: [ RUN ] NblibTraitsUtils.FuseTwo 8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 8: [ RUN ] NblibTraitsUtils.Fuse 8: [ OK ] NblibTraitsUtils.Fuse (0 ms) 8: [ RUN ] NblibTraitsUtils.Repeat 8: [ OK ] NblibTraitsUtils.Repeat (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 8: [ RUN ] NblibTraitsUtils.Contains 8: [ OK ] NblibTraitsUtils.Contains (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 8: [----------] 10 tests from NblibTraitsUtils (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 16 tests from 2 test suites ran. (0 ms total) 8: [ PASSED ] 16 tests. 8/94 Test #8: NbLibUtilTests ............................... Passed 0.08 sec test 9 Start 9: NbLibSetupTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 57 tests from 3 test suites. 9: [----------] Global test environment set-up. 9: [----------] 41 tests from NBlibTest 9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.CubicBoxWorks 9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 9: [ RUN ] NBlibTest.BoxEqual 9: [ OK ] NBlibTest.BoxEqual (0 ms) 9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 9: [ RUN ] NBlibTest.CanMergeInteractions 9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.PbcHolderWorks 9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 9: [ RUN ] NBlibTest.AtWorks 9: [ OK ] NBlibTest.AtWorks (0 ms) 9: [ RUN ] NBlibTest.AtThrows 9: [ OK ] NBlibTest.AtThrows (0 ms) 9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 9: [ RUN ] NBlibTest.CanAddInteractions 9: [ OK ] NBlibTest.CanAddInteractions (0 ms) 9: [ RUN ] NBlibTest.CanAddUreyBradley 9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 9: [ RUN ] NBlibTest.TopologyHasNumParticles 9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 9: [ RUN ] NBlibTest.TopologyHasCharges 9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 9: [ RUN ] NBlibTest.TopologyHasMasses 9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypes 9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 9: [ RUN ] NBlibTest.TopologyHasExclusions 9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 9: [ RUN ] NBlibTest.TopologyHasSequencing 9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 9: [ RUN ] NBlibTest.TopologyCanAggregateBonds 9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 9: [ RUN ] NBlibTest.TopologySequenceIdThrows 9: No particle O-Atom in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractions 9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 9: No particle Iron in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 9: [----------] 41 tests from NBlibTest (1 ms total) 9: 9: [----------] 15 tests from NbnxmSetupTest 9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.updateForcerecWorks 9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 9: [----------] 15 tests from NbnxmSetupTest (0 ms total) 9: 9: [----------] 1 test from VirialsTest 9: [ RUN ] VirialsTest.computeVirialTensorWorks 9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 9: [----------] 1 test from VirialsTest (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 57 tests from 3 test suites ran. (1 ms total) 9: [ PASSED ] 57 tests. 9/94 Test #9: NbLibSetupTests .............................. Passed 0.09 sec test 10 Start 10: NbLibTprTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibTprTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 10: Test timeout computed to be: 30 10: [==========] Running 4 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 4 tests from TprReaderTest 10: [ RUN ] TprReaderTest.SimDBTprIsCreated 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.SimDBTprIsCreated (30 ms) 10: [ RUN ] TprReaderTest.Spc2Reads 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Generating 1-4 interactions: fudge = 0.5 10: Number of degrees of freedom in T-Coupling group System is 9.00 10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: NVE simulation: will use the initial temperature of 2573.591 K for 10: determining the Verlet buffer size 10: 10: 10: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: You are using a plain Coulomb cut-off, which might produce artifacts. 10: You might want to consider using PME electrostatics. 10: 10: 10: 10: There were 4 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 3 of the 3 non-bonded parameter combinations 10: 10: Generated 3 of the 3 1-4 parameter combinations 10: 10: Excluding 2 bonded neighbours molecule type 'SOL' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.Spc2Reads (28 ms) 10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (20 ms) 10: [ RUN ] TprReaderTest.FCfromTprDataWorks 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 10: [----------] 4 tests from TprReaderTest (95 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 4 tests from 1 test suite ran. (99 ms total) 10: [ PASSED ] 4 tests. 10/94 Test #10: NbLibTprTests ................................ Passed 0.18 sec test 11 Start 11: NbLibIntegrationTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 11: Test timeout computed to be: 600 11: [==========] Running 20 tests from 1 test suite. 11: [----------] Global test environment set-up. 11: [----------] 20 tests from NBlibTest 11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ExpectedNumberOfForces 11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 11: [ RUN ] NBlibTest.CanIntegrateSystem 11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 11: [ RUN ] NBlibTest.UpdateChangesForces 11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.CanConstructSimulationState 11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanMove 11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanAssign 11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasBox 11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 11: [----------] 20 tests from NBlibTest (3 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 20 tests from 1 test suite ran. (3 ms total) 11: [ PASSED ] 20 tests. 11/94 Test #11: NbLibIntegrationTests ........................ Passed 0.27 sec test 12 Start 12: NbLibIntegratorTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 12: Test timeout computed to be: 600 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from NBlibTest 12: [ RUN ] NBlibTest.IntegratorWorks 12: [ OK ] NBlibTest.IntegratorWorks (0 ms) 12: [----------] 1 test from NBlibTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (0 ms total) 12: [ PASSED ] 1 test. 12/94 Test #12: NbLibIntegratorTests ......................... Passed 0.32 sec test 13 Start 13: TestUtilsUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests 13: Test timeout computed to be: 30 13: [==========] Running 75 tests from 7 test suites. 13: [----------] Global test environment set-up. 13: [----------] 10 tests from InteractiveTestHelperTest 13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 13: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 13: 13: [----------] 10 tests from NameOfTestFromTupleTest 13: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 13: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 13: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 13: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 13: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 13: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 13: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 13: 13: [----------] 3 tests from RefDataFilenameMakerTest 13: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 13: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 13: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 13: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 13: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 13: 13: [----------] 37 tests from ReferenceDataTest 13: [ RUN ] ReferenceDataTest.HandlesSimpleData 13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringBlockData 13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesVectorData 13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceData 13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectData 13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingData 13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedData 13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnys 13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesReadingValues 13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 13: [----------] 37 tests from ReferenceDataTest (2 ms total) 13: 13: [----------] 7 tests from FloatingPointDifferenceTest 13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 13: 13: [----------] 4 tests from FloatingPointToleranceTest 13: [ RUN ] FloatingPointToleranceTest.UlpTolerance 13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 13: 13: [----------] 4 tests from XvgTests 13: [ RUN ] XvgTests.CreateFile 13: [ OK ] XvgTests.CreateFile (0 ms) 13: [ RUN ] XvgTests.CheckMissing 13: [ OK ] XvgTests.CheckMissing (0 ms) 13: [ RUN ] XvgTests.CheckExtra 13: [ OK ] XvgTests.CheckExtra (0 ms) 13: [ RUN ] XvgTests.ReadIncorrect 13: [ OK ] XvgTests.ReadIncorrect (0 ms) 13: [----------] 4 tests from XvgTests (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 75 tests from 7 test suites ran. (5 ms total) 13: [ PASSED ] 75 tests. 13/94 Test #13: TestUtilsUnitTests ........................... Passed 0.26 sec test 14 Start 14: TestUtilsMpiUnitTests 14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests 14: Test timeout computed to be: 30 14: [==========] Running 1 test from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 1 test from MpiSelfTest 14: [ RUN ] MpiSelfTest.Runs 14: [ OK ] MpiSelfTest.Runs (0 ms) 14: [----------] 1 test from MpiSelfTest (0 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 1 test from 1 test suite ran. (0 ms total) 14: [ PASSED ] 1 test. 14/94 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.56 sec test 15 Start 15: UtilityUnitTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests 15: Test timeout computed to be: 30 15: [==========] Running 420 tests from 65 test suites. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.Move 15: [ OK ] AllocatorTest/0.Move (0 ms) 15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/0.Comparison 15: [ OK ] AllocatorTest/0.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/0 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.Move 15: [ OK ] AllocatorTest/1.Move (0 ms) 15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/1.Comparison 15: [ OK ] AllocatorTest/1.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/1 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.Move 15: [ OK ] AllocatorTest/2.Move (0 ms) 15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/2.Comparison 15: [ OK ] AllocatorTest/2.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/2 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.Move 15: [ OK ] AllocatorTest/3.Move (0 ms) 15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/3.Comparison 15: [ OK ] AllocatorTest/3.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/3 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.Move 15: [ OK ] AllocatorTest/4.Move (0 ms) 15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/4.Comparison 15: [ OK ] AllocatorTest/4.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/4 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.Move 15: [ OK ] AllocatorTest/5.Move (0 ms) 15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/5.Comparison 15: [ OK ] AllocatorTest/5.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/5 (0 ms total) 15: 15: [----------] 1 test from AllocatorUntypedTest 15: [ RUN ] AllocatorUntypedTest.Comparison 15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 15: [----------] 1 test from AllocatorUntypedTest (0 ms total) 15: 15: [----------] 4 tests from EmptyArrayRefTest 15: [ RUN ] EmptyArrayRefTest.IsEmpty 15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 15: 15: [----------] 1 test from EmptyConstArrayRefTest 15: [ RUN ] EmptyConstArrayRefTest.IsEmpty 15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 15: 15: [----------] 8 tests from BoolType 15: [ RUN ] BoolType.ImplicitConversion 15: [ OK ] BoolType.ImplicitConversion (0 ms) 15: [ RUN ] BoolType.FalseByDefault 15: [ OK ] BoolType.FalseByDefault (0 ms) 15: [ RUN ] BoolType.Assignment 15: [ OK ] BoolType.Assignment (0 ms) 15: [ RUN ] BoolType.Copy 15: [ OK ] BoolType.Copy (0 ms) 15: [ RUN ] BoolType.ArrayRefCanBeCreated 15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 15: [ RUN ] BoolType.CanBeCastToBool 15: [ OK ] BoolType.CanBeCastToBool (0 ms) 15: [ RUN ] BoolType.HasSizeOfBool 15: [ OK ] BoolType.HasSizeOfBool (0 ms) 15: [ RUN ] BoolType.HasAlignmentOfBool 15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 15: [----------] 8 tests from BoolType (0 ms total) 15: 15: [----------] 4 tests from ArrayRefFromBoolTypeVector 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.Works 15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 15: 15: [----------] 7 tests from CStringUtilityTest 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 15: [ RUN ] CStringUtilityTest.strip_comment 15: [ OK ] CStringUtilityTest.strip_comment (0 ms) 15: [ RUN ] CStringUtilityTest.upstring 15: [ OK ] CStringUtilityTest.upstring (0 ms) 15: [ RUN ] CStringUtilityTest.ltrim 15: [ OK ] CStringUtilityTest.ltrim (0 ms) 15: [ RUN ] CStringUtilityTest.rtrim 15: [ OK ] CStringUtilityTest.rtrim (0 ms) 15: [ RUN ] CStringUtilityTest.trim 15: [ OK ] CStringUtilityTest.trim (0 ms) 15: [----------] 7 tests from CStringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from DefaultInitializationAllocator 15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 15: 15: [----------] 4 tests from EnumerationHelpersTest 15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 15: 15: [----------] 1 test from EnumClassSuitsEnumerationArray 15: [ RUN ] EnumClassSuitsEnumerationArray.Works 15: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 15: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 15: 15: [----------] 18 tests from FixedCapacityVectorTest 15: [ RUN ] FixedCapacityVectorTest.IsEmpty 15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 15: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PushWorks 15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PopWorks 15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ResizeWorks 15: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ClearWorks 15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.AtThrows 15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 15: [ RUN ] FixedCapacityVectorTest.IteratorWorks 15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 15: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 15: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.DataWorks 15: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 15: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 15: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 15: 15: [----------] 5 tests from InMemorySerializerTest 15: [ RUN ] InMemorySerializerTest.Roundtrip 15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SizeIsCorrect 15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 15: [----------] 5 tests from InMemorySerializerTest (0 ms total) 15: 15: [----------] 4 tests from KeyValueTreeSerializerTest 15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 15: 15: [----------] 7 tests from TreeValueTransformTest 15: [ RUN ] TreeValueTransformTest.SimpleTransforms 15: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromString 15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 15: [ RUN ] TreeValueTransformTest.ScopedTransformRules 15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 15: [----------] 7 tests from TreeValueTransformTest (0 ms total) 15: 15: [----------] 1 test from TreeValueTransformErrorTest 15: [ RUN ] TreeValueTransformErrorTest.ConversionError 15: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 15: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 15: 15: [----------] 9 tests from ListOfLists 15: [ RUN ] ListOfLists.EmptyListOfListsWorks 15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 15: [ RUN ] ListOfLists.AppendWorks 15: [ OK ] ListOfLists.AppendWorks (0 ms) 15: [ RUN ] ListOfLists.EmptyListWorks 15: [ OK ] ListOfLists.EmptyListWorks (0 ms) 15: [ RUN ] ListOfLists.AppendAccessWorks 15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 15: [ RUN ] ListOfLists.ClearWorks 15: [ OK ] ListOfLists.ClearWorks (0 ms) 15: [ RUN ] ListOfLists.OutOfRangeAccessThrows 15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 15: [ RUN ] ListOfLists.FrontAndBackWork 15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 15: [ RUN ] ListOfLists.ExtractsAndRestores 15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 15: [----------] 9 tests from ListOfLists (0 ms total) 15: 15: [----------] 7 tests from LoggerTest 15: [ RUN ] LoggerTest.EmptyLoggerWorks 15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToStream 15: [ OK ] LoggerTest.LogsToStream (0 ms) 15: [ RUN ] LoggerTest.LogsToFile 15: [ OK ] LoggerTest.LogsToFile (0 ms) 15: [ RUN ] LoggerTest.LevelFilteringWorks 15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleStreams 15: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleFiles 15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 15: [ RUN ] LoggerTest.LogsToStreamAndFile 15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 15: [----------] 7 tests from LoggerTest (0 ms total) 15: 15: [----------] 7 tests from MessageStringCollectorTest 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveAssign 15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 15: 15: [----------] 1 test from PathTest 15: [ RUN ] PathTest.StripSourcePrefixWorks 15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 15: [----------] 1 test from PathTest (0 ms total) 15: 15: [----------] 2 tests from PhysicalNodeCommunicatorTest 15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 15: 15: [----------] 5 tests from Range 15: [ RUN ] Range.EmptyRangeWorks 15: [ OK ] Range.EmptyRangeWorks (0 ms) 15: [ RUN ] Range.NonEmptyRangeWorks 15: [ OK ] Range.NonEmptyRangeWorks (0 ms) 15: [ RUN ] Range.BeginEnd 15: [ OK ] Range.BeginEnd (0 ms) 15: [ RUN ] Range.IsInRangeWorks 15: [ OK ] Range.IsInRangeWorks (0 ms) 15: [ RUN ] Range.IteratorWorks 15: [ OK ] Range.IteratorWorks (0 ms) 15: [----------] 5 tests from Range (0 ms total) 15: 15: [----------] 3 tests from ScopeGuardTest 15: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 15: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 15: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 15: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 15: [----------] 3 tests from ScopeGuardTest (0 ms total) 15: 15: [----------] 7 tests from StringConvert 15: [ RUN ] StringConvert.NoResultFromEptyString 15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 15: [ RUN ] StringConvert.ThreeFloatsSuccessfully 15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 15: [ RUN ] StringConvert.OneIntSucessfully 15: [ OK ] StringConvert.OneIntSucessfully (0 ms) 15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 15: [ RUN ] StringConvert.ThrowsWhenWrongSize 15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 15: [----------] 7 tests from StringConvert (0 ms total) 15: 15: [----------] 7 tests from StringToEnumValueConverterTest 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 15: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 15: 15: [----------] 9 tests from StringUtilityTest 15: [ RUN ] StringUtilityTest.StartsWith 15: [ OK ] StringUtilityTest.StartsWith (0 ms) 15: [ RUN ] StringUtilityTest.EndsWith 15: [ OK ] StringUtilityTest.EndsWith (0 ms) 15: [ RUN ] StringUtilityTest.StripSuffixIfPresent 15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 15: [ RUN ] StringUtilityTest.StripString 15: [ OK ] StringUtilityTest.StripString (0 ms) 15: [ RUN ] StringUtilityTest.SplitString 15: [ OK ] StringUtilityTest.SplitString (0 ms) 15: [ RUN ] StringUtilityTest.SplitDelimitedString 15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 15: [----------] 9 tests from StringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from FormatStringTest 15: [ RUN ] FormatStringTest.HandlesBasicFormatting 15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 15: [ RUN ] FormatStringTest.HandlesLongStrings 15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 15: [----------] 2 tests from FormatStringTest (0 ms total) 15: 15: [----------] 1 test from StringFormatterTest 15: [ RUN ] StringFormatterTest.HandlesBasicFormatting 15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 15: [----------] 1 test from StringFormatterTest (0 ms total) 15: 15: [----------] 1 test from formatAndJoinTest 15: [ RUN ] formatAndJoinTest.Works 15: [ OK ] formatAndJoinTest.Works (0 ms) 15: [----------] 1 test from formatAndJoinTest (0 ms total) 15: 15: [----------] 1 test from JoinStringsTest 15: [ RUN ] JoinStringsTest.Works 15: [ OK ] JoinStringsTest.Works (0 ms) 15: [----------] 1 test from JoinStringsTest (0 ms total) 15: 15: [----------] 6 tests from ReplaceAllTest 15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesNoMatches 15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 15: [----------] 6 tests from ReplaceAllTest (0 ms total) 15: 15: [----------] 10 tests from TextLineWrapperTest 15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectly 15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndent 15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 15: [----------] 10 tests from TextLineWrapperTest (0 ms total) 15: 15: [----------] 1 test from CompileTimeStringJoin 15: [ RUN ] CompileTimeStringJoin.Works 15: [ OK ] CompileTimeStringJoin.Works (0 ms) 15: [----------] 1 test from CompileTimeStringJoin (0 ms total) 15: 15: [----------] 3 tests from TemplateMPTest 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 15: [----------] 3 tests from TemplateMPTest (0 ms total) 15: 15: [----------] 6 tests from TextWriterTest 15: [ RUN ] TextWriterTest.WritesLines 15: [ OK ] TextWriterTest.WritesLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInParts 15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 15: [ RUN ] TextWriterTest.WritesWrappedLines 15: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 15: [ RUN ] TextWriterTest.TracksNewlines 15: [ OK ] TextWriterTest.TracksNewlines (0 ms) 15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 15: [----------] 6 tests from TextWriterTest (0 ms total) 15: 15: [----------] 1 test from TypeTraitsTest 15: [ RUN ] TypeTraitsTest.IsIntegralConstant 15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 15: [----------] 1 test from TypeTraitsTest (0 ms total) 15: 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 15: 15: [----------] 11 tests from WithInputPaths/PathSearchTest 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 15: 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 420 tests from 65 test suites ran. (5 ms total) 15: [ PASSED ] 420 tests. 15: 15: YOU HAVE 1 DISABLED TEST 15: 15/94 Test #15: UtilityUnitTests ............................. Passed 0.31 sec test 16 Start 16: UtilityMpiUnitTests 16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests 16: Test timeout computed to be: 30 16: [==========] Running 2 tests from 1 test suite. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from PhysicalNodeCommunicatorTest 16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (6 ms) 16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 16: [----------] 2 tests from PhysicalNodeCommunicatorTest (7 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 2 tests from 1 test suite ran. (7 ms total) 16: [ PASSED ] 2 tests. 16/94 Test #16: UtilityMpiUnitTests .......................... Passed 0.44 sec test 17 Start 17: GmxlibTests 17: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxlibTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests 17: Test timeout computed to be: 30 17: [==========] Running 78 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 72 tests from NBInteraction/NonbondedFepTest 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 17: [----------] 72 tests from NBInteraction/NonbondedFepTest (5 ms total) 17: 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 78 tests from 2 test suites ran. (6 ms total) 17: [ PASSED ] 78 tests. 17/94 Test #17: GmxlibTests .................................. Passed 0.10 sec test 18 Start 18: MdlibUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests 18: Test timeout computed to be: 30 18: [==========] Running 1032 tests from 27 test suites. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from EffectiveAtomDensity 18: [ RUN ] EffectiveAtomDensity.VolumeIndependence 18: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 18: [ RUN ] EffectiveAtomDensity.WeightingWorks 18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 18: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 18: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 18: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 18: 18: [----------] 2 tests from AtomNonbondedAndKineticProperties 18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 18: 18: [----------] 1 test from VerletBufferConstraintTest 18: [ RUN ] VerletBufferConstraintTest.EqualMasses 18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 18: 18: [----------] 1 test from VerletBufferSize 18: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 18: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 18: [----------] 1 test from VerletBufferSize (0 ms total) 18: 18: [----------] 6 tests from CalcvirTest 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 18: [----------] 6 tests from CalcvirTest (0 ms total) 18: 18: [----------] 2 tests from PrEbinTest 18: [ RUN ] PrEbinTest.HandlesAverages 18: [ OK ] PrEbinTest.HandlesAverages (0 ms) 18: [ RUN ] PrEbinTest.HandlesEmptyAverages 18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 18: [----------] 2 tests from PrEbinTest (0 ms total) 18: 18: [----------] 3 tests from EnergyDriftTracker 18: [ RUN ] EnergyDriftTracker.emptyWorks 18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.onePointWorks 18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.manyPointsWorks 18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 18: [----------] 3 tests from EnergyDriftTracker (0 ms total) 18: 18: [----------] 4 tests from ShakeTest 18: [ RUN ] ShakeTest.ConstrainsOneBond 18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 18: [----------] 4 tests from ShakeTest (0 ms total) 18: 18: [----------] 1 test from NullSignalTest 18: [ RUN ] NullSignalTest.NullSignallerWorks 18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 18: [----------] 1 test from NullSignalTest (0 ms total) 18: 18: [----------] 7 tests from SignalTest 18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 18: [----------] 7 tests from SignalTest (0 ms total) 18: 18: [----------] 13 tests from UpdateGroupsTest 18: [ RUN ] UpdateGroupsTest.WithEthaneUA 18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 18: [ RUN ] UpdateGroupsTest.WithMethane 18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithEthane 18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFourSite 18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 18: [----------] 13 tests from UpdateGroupsTest (0 ms total) 18: 18: [----------] 1 test from UpdateGroupsCog 18: [ RUN ] UpdateGroupsCog.ComputesCogs 18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 18: [----------] 1 test from UpdateGroupsCog (0 ms total) 18: 18: [----------] 2 tests from WholeMoleculeTransform 18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 18: [ RUN ] WholeMoleculeTransform.HandlesReordering 18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 18: 18: [----------] 28 tests from WithParameters/ConstraintsTest 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 18: [----------] 28 tests from WithParameters/ConstraintsTest (14 ms total) 18: 18: [----------] 11 tests from WithParameters/EnergyOutputTest 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (3 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (2 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 18: [----------] 11 tests from WithParameters/EnergyOutputTest (15 ms total) 18: 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 18: 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 18: 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 18: 18: [----------] 17 tests from WithParameters/LangevinTest 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 18: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 18: 18: [----------] 16 tests from WithParameters/LeapFrogTest 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (3 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 18: [----------] 16 tests from WithParameters/LeapFrogTest (12 ms total) 18: 18: [----------] 140 tests from Cubic/ParrRahmTest 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Cubic/ParrRahmTest (4 ms total) 18: 18: [----------] 140 tests from Rectilinear/ParrRahmTest 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Rectilinear/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (1 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (4 ms total) 18: 18: [----------] 140 tests from TruncOct/ParrRahmTest 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (1 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from TruncOct/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from Other/ParrRahmTest 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Other/ParrRahmTest (5 ms total) 18: 18: [----------] 13 tests from WithParameters/SettleTest 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 18: [----------] 13 tests from WithParameters/SettleTest (4 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1032 tests from 27 test suites ran. (84 ms total) 18: [ PASSED ] 1032 tests. 18/94 Test #18: MdlibUnitTest ................................ Passed 0.21 sec test 19 Start 19: AwhTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AwhTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests 19: Test timeout computed to be: 30 19: [==========] Running 25 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from SerializationTest 19: [ RUN ] SerializationTest.CanSerializeDimParams 19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeBiasParams 19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeAwhParams 19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 19: [----------] 3 tests from SerializationTest (0 ms total) 19: 19: [----------] 1 test from BiasTest 19: [ RUN ] BiasTest.DetectsCovering 19: [ OK ] BiasTest.DetectsCovering (0 ms) 19: [----------] 1 test from BiasTest (0 ms total) 19: 19: [----------] 1 test from biasGridTest 19: [ RUN ] biasGridTest.neighborhood 19: [ OK ] biasGridTest.neighborhood (0 ms) 19: [----------] 1 test from biasGridTest (0 ms total) 19: 19: [----------] 2 tests from BiasFepLambdaStateTest 19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 19: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 19: 19: [----------] 8 tests from WithParameters/BiasTest 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 19: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 19: 19: [----------] 2 tests from WithParameters/BiasStateTest 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 19: 19: [----------] 1 test from WithParameters/UserInputTest 19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 19: 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (15 ms total) 19: 19: [----------] 3 tests from WithParameters/FrictionMetricTest 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) 19: [----------] 3 tests from WithParameters/FrictionMetricTest (13 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 25 tests from 9 test suites ran. (35 ms total) 19: [ PASSED ] 25 tests. 19/94 Test #19: AwhTest ...................................... Passed 0.33 sec test 20 Start 20: DensityFittingAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 2 tests from DensityFittingTest 20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 20: [ RUN ] DensityFittingTest.SingleAtom 20: [ OK ] DensityFittingTest.SingleAtom (0 ms) 20: [----------] 2 tests from DensityFittingTest (1 ms total) 20: 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest 20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 20: 20: [----------] 1 test from DensityFittingForceProviderState 20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 20: 20: [----------] 8 tests from DensityFittingOptionsTest 20: [ RUN ] DensityFittingOptionsTest.DefaultParameters 20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 20: [ RUN ] DensityFittingOptionsTest.KvtToInternal 20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 4 test suites ran. (1 ms total) 20: [ PASSED ] 18 tests. 20/94 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.08 sec test 21 Start 21: QMMMAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests 21: Test timeout computed to be: 30 21: [==========] Running 21 tests from 5 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from QMMMInputGeneratorTest 21: [ RUN ] QMMMInputGeneratorTest.CanConstruct 21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 21: 21: [----------] 7 tests from QMMMTopologyPreprocessorTest 21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -201949793 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -1076449634 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -8723 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (7 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -3948725 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (7 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to 2120220661 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (8 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 45.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -34115599 21: 21: Generated 3 of the 6 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'VSTEST' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 21: 21: Cleaning up constraints and constant bonded interactions with virtual sites 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) 21: [----------] 7 tests from QMMMTopologyPreprocessorTest (31 ms total) 21: 21: [----------] 9 tests from QMMMOptionsTest 21: [ RUN ] QMMMOptionsTest.DefaultParameters 21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] QMMMOptionsTest.OptionSetsActive 21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 21: [----------] 9 tests from QMMMOptionsTest (0 ms total) 21: 21: [----------] 1 test from QMMMForceProviderTest 21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 21: [----------] 1 test from QMMMForceProviderTest (0 ms total) 21: 21: [----------] 1 test from QMMMTest 21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from QMMMTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 21 tests from 5 test suites ran. (33 ms total) 21: [ PASSED ] 21 tests. 21/94 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.19 sec test 22 Start 22: ColvarsAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests 22: Test timeout computed to be: 30 22: [==========] Running 16 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 1 test from ColvarsTest 22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 22: [----------] 1 test from ColvarsTest (0 ms total) 22: 22: [----------] 6 tests from ColvarsOptionsTest 22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OptionSetsActive 22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -541630465 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (6 ms) 22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 22: [----------] 6 tests from ColvarsOptionsTest (6 ms total) 22: 22: [----------] 4 tests from ColvarsPreProcessorTest 22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -1361189921 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (3 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to 1306256988 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -646650401 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -1779696333 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 22: [----------] 4 tests from ColvarsPreProcessorTest (14 ms total) 22: 22: [----------] 5 tests from ColvarsForceProviderTest 22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 22: [ RUN ] ColvarsForceProviderTest.SimpleInputs 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -1546651657 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.SimpleInputs (7 ms) 22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -305201537 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (7 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -2728131 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (46 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 66.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: NVE simulation: will use the initial temperature of 300.368 K for 22: determining the Verlet buffer size 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -1654656769 22: 22: Generated 2211 of the 2211 non-bonded parameter combinations 22: 22: Generated 2211 of the 2211 1-4 parameter combinations 22: 22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 22: Analysing residue names: 22: There are: 2 Protein residues 22: Analysing Protein... 22: 22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 22: 22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 22: 22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 22: 22: Note that mdrun will redetermine rlist based on the actual pair-list setup 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (64 ms) 22: [----------] 5 tests from ColvarsForceProviderTest (126 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 16 tests from 4 test suites ran. (147 ms total) 22: [ PASSED ] 16 tests. 22/94 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.36 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from NNPotTest (0 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (0 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -369115205 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -68157507 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -319819284 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (7 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to 2004856309 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (12 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (25 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (26 ms total) 23: [ PASSED ] 12 tests. 23/94 Test #23: NNPotAppliedForcesUnitTest ................... Passed 0.35 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (0 ms total) 24: [ PASSED ] 3 tests. 24/94 Test #24: AppliedForcesUnitTest ........................ Passed 0.17 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (2 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (2 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (12 ms total) 25: [ PASSED ] 132 tests. 25/94 Test #25: ListedForcesTest ............................. Passed 0.18 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 383 tests from 4 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (0 ms total) 26: 26: [----------] 2 tests from SimdEnergyAccumulatorTest 26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 26: 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (6 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (7 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (6 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (6 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (400 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 383 tests from 4 test suites ran. (401 ms total) 26: [ PASSED ] 185 tests. 26: [ SKIPPED ] 198 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/94 Test #26: NbnxmTests ................................... Passed 0.70 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/94 Test #27: NbnxmGpuTests ................................ Passed 0.14 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (1 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (4 ms total) 28: [ PASSED ] 60 tests. 28/94 Test #28: CommandLineUnitTests ......................... Passed 0.12 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/94 Test #29: DomDecTests .................................. Passed 0.07 sec test 30 Start 30: DomDecMpiTests 30: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (3 ms) 30: [----------] 4 tests from HaloExchangeTest (55 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (55 ms total) 30: [ PASSED ] 4 tests. 30/94 Test #30: DomDecMpiTests ............................... Passed 0.59 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (94 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from Pme_SolveTest (8 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (5 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (8 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (4 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [----------] 72 tests from Pme_GatherTest (13 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (8 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (29 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (165 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/94 Test #31: EwaldUnitTests ............................... Passed 0.26 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (3 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (4 ms) 32: [----------] 2 tests from ManyFFTTest (7 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 32: [----------] 1 test from FFTTest (1 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (3 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (8 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (19 ms total) 32: [ PASSED ] 15 tests. 32/94 Test #32: FFTUnitTests ................................. Passed 0.10 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (0 ms total) 33: [ PASSED ] 67 tests. 33/94 Test #33: GpuUtilsUnitTests ............................ Passed 0.08 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (0 ms) 34: [----------] 1 test from CpuInfoTest (0 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (4 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (4 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (4 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (3 ms) 34: [----------] 4 tests from HardwareTopologyTest (16 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (27 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/94 Test #34: HardwareUnitTests ............................ Passed 0.10 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (0 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (12 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (12 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (26 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (11 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 35: [----------] 2 tests from NelderMead (11 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (42 ms total) 35: [ PASSED ] 328 tests. 35/94 Test #35: MathUnitTests ................................ Passed 0.12 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 36: [----------] 17 tests from ThreadAffinityTest (4 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (4 ms total) 36: [ PASSED ] 21 tests. 36/94 Test #36: MdrunUtilityUnitTests ........................ Passed 0.07 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (83 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (52 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (64 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (63 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (80 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (16 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (431 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (36 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (37 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (473 ms total) 37: [ PASSED ] 13 tests. 37/94 Test #37: MdrunUtilityMpiUnitTests ..................... Passed 1.06 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (0 ms total) 38: [ PASSED ] 32 tests. 38/94 Test #38: MDSpanTests .................................. Passed 0.21 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 39: [----------] 2 tests from CheckpointDataTest (3 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (0 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (4 ms total) 39: [ PASSED ] 97 tests. 39/94 Test #39: MdtypesUnitTest .............................. Passed 0.12 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (0 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 40: [----------] 3 tests from HelpManagerTest (0 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 40: [----------] 11 tests from HelpWriterContextTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (1 ms total) 40: [ PASSED ] 22 tests. 40/94 Test #40: OnlineHelpUnitTests .......................... Passed 0.07 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (0 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (0 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (2 ms total) 41: [ PASSED ] 112 tests. 41/94 Test #41: OptionsUnitTests ............................. Passed 0.13 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 37 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (0 ms total) 42: 42: [----------] 5 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 42: [----------] 5 tests from PbcTest (0 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 37 tests from 5 test suites ran. (3 ms total) 42: [ PASSED ] 37 tests. 42/94 Test #42: PbcutilUnitTest .............................. Passed 0.12 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (0 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (0 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (0 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (1 ms total) 43: [ PASSED ] 44 tests. 43/94 Test #43: RandomUnitTests .............................. Passed 0.26 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (0 ms total) 44: [ PASSED ] 1 test. 44/94 Test #44: RestraintTests ............................... Passed 0.07 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 20 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (0 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (6 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (9 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 45: [ RUN ] SplineTableTest/0.Simd 45: [ OK ] SplineTableTest/0.Simd (2 ms) 45: [ RUN ] SplineTableTest/0.SimdTwoFunctions 45: [ OK ] SplineTableTest/0.SimdTwoFunctions (8 ms) 45: [----------] 10 tests from SplineTableTest/0 (39 ms total) 45: 45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (0 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (0 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 45: [ RUN ] SplineTableTest/1.Simd 45: [ OK ] SplineTableTest/1.Simd (0 ms) 45: [ RUN ] SplineTableTest/1.SimdTwoFunctions 45: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 45: [----------] 10 tests from SplineTableTest/1 (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 20 tests from 2 test suites ran. (45 ms total) 45: [ PASSED ] 20 tests. 45/94 Test #45: TableUnitTests ............................... Passed 0.12 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (0 ms total) 46: [ PASSED ] 3 tests. 46/94 Test #46: TaskAssignmentUnitTests ...................... Passed 0.07 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (1 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (1 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (1 ms total) 47: [ PASSED ] 6 tests. 47/94 Test #47: GmxTimingTests ............................... Passed 0.09 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (1 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 48: [----------] 3 tests from IndexTest (5 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (0 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (0 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (5 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (12 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/94 Test #48: TopologyTest ................................. Passed 0.31 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (0 ms total) 49: [ PASSED ] 10 tests. 49/94 Test #49: PullTest ..................................... Passed 0.22 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 288 tests from 22 test suites. 50: [----------] Global test environment set-up. 50: [----------] 9 tests from SimdBootstrapTest 50: [ RUN ] SimdBootstrapTest.loadStore 50: [ OK ] SimdBootstrapTest.loadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.loadU 50: [ OK ] SimdBootstrapTest.loadU (0 ms) 50: [ RUN ] SimdBootstrapTest.storeU 50: [ OK ] SimdBootstrapTest.storeU (0 ms) 50: [ RUN ] SimdBootstrapTest.loadStoreI 50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 50: [ RUN ] SimdBootstrapTest.loadUI 50: [ OK ] SimdBootstrapTest.loadUI (0 ms) 50: [ RUN ] SimdBootstrapTest.storeUI 50: [ OK ] SimdBootstrapTest.storeUI (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadStore 50: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadU 50: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4StoreU 50: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 50: [----------] 9 tests from SimdBootstrapTest (0 ms total) 50: 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (0 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (0 ms total) 50: 50: [----------] 1 test from SimdTest 50: [ RUN ] SimdTest.GmxAligned 50: [ OK ] SimdTest.GmxAligned (0 ms) 50: [----------] 1 test from SimdTest (0 ms total) 50: 50: [----------] 42 tests from SimdFloatingpointTest 50: [ RUN ] SimdFloatingpointTest.setZero 50: [ OK ] SimdFloatingpointTest.setZero (0 ms) 50: [ RUN ] SimdFloatingpointTest.set 50: [ OK ] SimdFloatingpointTest.set (0 ms) 50: [ RUN ] SimdFloatingpointTest.add 50: [ OK ] SimdFloatingpointTest.add (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskAdd 50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 50: [ RUN ] SimdFloatingpointTest.sub 50: [ OK ] SimdFloatingpointTest.sub (0 ms) 50: [ RUN ] SimdFloatingpointTest.mul 50: [ OK ] SimdFloatingpointTest.mul (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzMul 50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 50: [ RUN ] SimdFloatingpointTest.fma 50: [ OK ] SimdFloatingpointTest.fma (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzFma 50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fms 50: [ OK ] SimdFloatingpointTest.fms (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnma 50: [ OK ] SimdFloatingpointTest.fnma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnms 50: [ OK ] SimdFloatingpointTest.fnms (0 ms) 50: [ RUN ] SimdFloatingpointTest.abs 50: [ OK ] SimdFloatingpointTest.abs (0 ms) 50: [ RUN ] SimdFloatingpointTest.neg 50: [ OK ] SimdFloatingpointTest.neg (0 ms) 50: [ RUN ] SimdFloatingpointTest.and 50: [ OK ] SimdFloatingpointTest.and (0 ms) 50: [ RUN ] SimdFloatingpointTest.or 50: [ OK ] SimdFloatingpointTest.or (0 ms) 50: [ RUN ] SimdFloatingpointTest.xor 50: [ OK ] SimdFloatingpointTest.xor (0 ms) 50: [ RUN ] SimdFloatingpointTest.andNot 50: [ OK ] SimdFloatingpointTest.andNot (0 ms) 50: [ RUN ] SimdFloatingpointTest.max 50: [ OK ] SimdFloatingpointTest.max (0 ms) 50: [ RUN ] SimdFloatingpointTest.min 50: [ OK ] SimdFloatingpointTest.min (0 ms) 50: [ RUN ] SimdFloatingpointTest.round 50: [ OK ] SimdFloatingpointTest.round (0 ms) 50: [ RUN ] SimdFloatingpointTest.roundMode 50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 50: [ RUN ] SimdFloatingpointTest.trunc 50: [ OK ] SimdFloatingpointTest.trunc (0 ms) 50: [ RUN ] SimdFloatingpointTest.frexp 50: [ OK ] SimdFloatingpointTest.frexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.ldexp 50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.rsqrt 50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRsqrt 50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.rcp 50: [ OK ] SimdFloatingpointTest.rcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRcp 50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.selectByNotMask 50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpNe 50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLe 50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLt 50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 50: [ RUN ] SimdFloatingpointTest.testBits 50: [ OK ] SimdFloatingpointTest.testBits (0 ms) 50: [ RUN ] SimdFloatingpointTest.andB 50: [ OK ] SimdFloatingpointTest.andB (0 ms) 50: [ RUN ] SimdFloatingpointTest.orB 50: [ OK ] SimdFloatingpointTest.orB (0 ms) 50: [ RUN ] SimdFloatingpointTest.anyTrueB 50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 50: [ RUN ] SimdFloatingpointTest.blend 50: [ OK ] SimdFloatingpointTest.blend (0 ms) 50: [ RUN ] SimdFloatingpointTest.reduce 50: [ OK ] SimdFloatingpointTest.reduce (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 50: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 50: 50: [----------] 16 tests from SimdFloatingpointUtilTest 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 50: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 50: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 50: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 50: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 50: 50: [----------] 23 tests from SimdIntegerTest 50: [ RUN ] SimdIntegerTest.setZero 50: [ OK ] SimdIntegerTest.setZero (0 ms) 50: [ RUN ] SimdIntegerTest.set 50: [ OK ] SimdIntegerTest.set (0 ms) 50: [ RUN ] SimdIntegerTest.add 50: [ OK ] SimdIntegerTest.add (0 ms) 50: [ RUN ] SimdIntegerTest.sub 50: [ OK ] SimdIntegerTest.sub (0 ms) 50: [ RUN ] SimdIntegerTest.mul 50: [ OK ] SimdIntegerTest.mul (0 ms) 50: [ RUN ] SimdIntegerTest.and 50: [ OK ] SimdIntegerTest.and (0 ms) 50: [ RUN ] SimdIntegerTest.andNot 50: [ OK ] SimdIntegerTest.andNot (0 ms) 50: [ RUN ] SimdIntegerTest.or 50: [ OK ] SimdIntegerTest.or (0 ms) 50: [ RUN ] SimdIntegerTest.xor 50: [ OK ] SimdIntegerTest.xor (0 ms) 50: [ RUN ] SimdIntegerTest.extract 50: [ OK ] SimdIntegerTest.extract (0 ms) 50: [ RUN ] SimdIntegerTest.cvtR2I 50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvttR2I 50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvtI2R 50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpLt 50: [ OK ] SimdIntegerTest.cmpLt (0 ms) 50: [ RUN ] SimdIntegerTest.testBits 50: [ OK ] SimdIntegerTest.testBits (0 ms) 50: [ RUN ] SimdIntegerTest.andB 50: [ OK ] SimdIntegerTest.andB (0 ms) 50: [ RUN ] SimdIntegerTest.orB 50: [ OK ] SimdIntegerTest.orB (0 ms) 50: [ RUN ] SimdIntegerTest.anyTrue 50: [ OK ] SimdIntegerTest.anyTrue (0 ms) 50: [ RUN ] SimdIntegerTest.blend 50: [ OK ] SimdIntegerTest.blend (0 ms) 50: [ RUN ] SimdIntegerTest.cvtB2IB 50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 50: [ RUN ] SimdIntegerTest.cvtIB2B 50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 50: [----------] 23 tests from SimdIntegerTest (0 ms total) 50: 50: [----------] 56 tests from SimdMathTest 50: [ RUN ] SimdMathTest.generateTestPointsFloat 50: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 50: [ RUN ] SimdMathTest.copysign 50: [ OK ] SimdMathTest.copysign (0 ms) 50: [ RUN ] SimdMathTest.invsqrt 50: [ OK ] SimdMathTest.invsqrt (0 ms) 50: [ RUN ] SimdMathTest.maskzInvsqrt 50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPair 50: [ OK ] SimdMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdMathTest.sqrt 50: [ OK ] SimdMathTest.sqrt (0 ms) 50: [ RUN ] SimdMathTest.sqrtUnsafe 50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 50: [ RUN ] SimdMathTest.inv 50: [ OK ] SimdMathTest.inv (0 ms) 50: [ RUN ] SimdMathTest.maskzInv 50: [ OK ] SimdMathTest.maskzInv (0 ms) 50: [ RUN ] SimdMathTest.cbrt 50: [ OK ] SimdMathTest.cbrt (0 ms) 50: [ RUN ] SimdMathTest.invcbrt 50: [ OK ] SimdMathTest.invcbrt (0 ms) 50: [ RUN ] SimdMathTest.log2 50: [ OK ] SimdMathTest.log2 (0 ms) 50: [ RUN ] SimdMathTest.log 50: [ OK ] SimdMathTest.log (0 ms) 50: [ RUN ] SimdMathTest.exp2 50: [ OK ] SimdMathTest.exp2 (0 ms) 50: [ RUN ] SimdMathTest.exp2Unsafe 50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 50: [ RUN ] SimdMathTest.exp 50: [ OK ] SimdMathTest.exp (0 ms) 50: [ RUN ] SimdMathTest.expUnsafe 50: [ OK ] SimdMathTest.expUnsafe (0 ms) 50: [ RUN ] SimdMathTest.pow 50: [ OK ] SimdMathTest.pow (0 ms) 50: [ RUN ] SimdMathTest.powUnsafe 50: [ OK ] SimdMathTest.powUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erf 50: [ OK ] SimdMathTest.erf (0 ms) 50: [ RUN ] SimdMathTest.erfc 50: [ OK ] SimdMathTest.erfc (0 ms) 50: [ RUN ] SimdMathTest.sin 50: [ OK ] SimdMathTest.sin (0 ms) 50: [ RUN ] SimdMathTest.cos 50: [ OK ] SimdMathTest.cos (0 ms) 50: [ RUN ] SimdMathTest.tan 50: [ OK ] SimdMathTest.tan (4 ms) 50: [ RUN ] SimdMathTest.asin 50: [ OK ] SimdMathTest.asin (0 ms) 50: [ RUN ] SimdMathTest.acos 50: [ OK ] SimdMathTest.acos (0 ms) 50: [ RUN ] SimdMathTest.atan 50: [ OK ] SimdMathTest.atan (0 ms) 50: [ RUN ] SimdMathTest.atan2 50: [ OK ] SimdMathTest.atan2 (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrection 50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrection 50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracy 50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.invSingleAccuracy 50: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cbrtSingleAccuracy 50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.log2SingleAccuracy 50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.logSingleAccuracy 50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracy 50: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracy 50: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracy 50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erfSingleAccuracy 50: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.erfcSingleAccuracy 50: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sinSingleAccuracy 50: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cosSingleAccuracy 50: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.tanSingleAccuracy 50: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.asinSingleAccuracy 50: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.acosSingleAccuracy 50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atanSingleAccuracy 50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atan2SingleAccuracy 50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 56 tests from SimdMathTest (19 ms total) 50: 50: [----------] 1 test from EmptyArrayRefTest 50: [ RUN ] EmptyArrayRefTest.IsEmpty 50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 50: [----------] 1 test from EmptyArrayRefTest (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/0.Assignment 50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/1.Assignment 50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/0.Basic 50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/1.Basic 50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 50: 50: [----------] 3 tests from SimdVectorOperationsTest 50: [ RUN ] SimdVectorOperationsTest.iprod 50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 50: [ RUN ] SimdVectorOperationsTest.norm2 50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 50: [ RUN ] SimdVectorOperationsTest.cprod 50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 50: 50: [----------] 32 tests from Simd4FloatingpointTest 50: [ RUN ] Simd4FloatingpointTest.setZero 50: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 50: [ RUN ] Simd4FloatingpointTest.set 50: [ OK ] Simd4FloatingpointTest.set (0 ms) 50: [ RUN ] Simd4FloatingpointTest.add 50: [ OK ] Simd4FloatingpointTest.add (0 ms) 50: [ RUN ] Simd4FloatingpointTest.sub 50: [ OK ] Simd4FloatingpointTest.sub (0 ms) 50: [ RUN ] Simd4FloatingpointTest.mul 50: [ OK ] Simd4FloatingpointTest.mul (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fma 50: [ OK ] Simd4FloatingpointTest.fma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fms 50: [ OK ] Simd4FloatingpointTest.fms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnma 50: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnms 50: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.abs 50: [ OK ] Simd4FloatingpointTest.abs (0 ms) 50: [ RUN ] Simd4FloatingpointTest.neg 50: [ OK ] Simd4FloatingpointTest.neg (0 ms) 50: [ RUN ] Simd4FloatingpointTest.and 50: [ OK ] Simd4FloatingpointTest.and (0 ms) 50: [ RUN ] Simd4FloatingpointTest.or 50: [ OK ] Simd4FloatingpointTest.or (0 ms) 50: [ RUN ] Simd4FloatingpointTest.xor 50: [ OK ] Simd4FloatingpointTest.xor (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andNot 50: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 50: [ RUN ] Simd4FloatingpointTest.max 50: [ OK ] Simd4FloatingpointTest.max (0 ms) 50: [ RUN ] Simd4FloatingpointTest.min 50: [ OK ] Simd4FloatingpointTest.min (0 ms) 50: [ RUN ] Simd4FloatingpointTest.round 50: [ OK ] Simd4FloatingpointTest.round (0 ms) 50: [ RUN ] Simd4FloatingpointTest.trunc 50: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 50: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 50: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.selectByNotMask 50: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpNe 50: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLe 50: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLt 50: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andB 50: [ OK ] Simd4FloatingpointTest.andB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.orB 50: [ OK ] Simd4FloatingpointTest.orB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.anyTrue 50: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 50: [ RUN ] Simd4FloatingpointTest.blend 50: [ OK ] Simd4FloatingpointTest.blend (0 ms) 50: [ RUN ] Simd4FloatingpointTest.reduce 50: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 50: [ RUN ] Simd4FloatingpointTest.dotProduct 50: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 50: [ RUN ] Simd4FloatingpointTest.transpose 50: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 50: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 50: 50: [----------] 2 tests from Simd4MathTest 50: [ RUN ] Simd4MathTest.invsqrt 50: [ OK ] Simd4MathTest.invsqrt (0 ms) 50: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 50: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 50: [----------] 2 tests from Simd4MathTest (0 ms total) 50: 50: [----------] 1 test from Simd4VectorOperationsTest 50: [ RUN ] Simd4VectorOperationsTest.norm2 50: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 50: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 288 tests from 22 test suites ran. (20 ms total) 50: [ PASSED ] 288 tests. 50/94 Test #50: SimdUnitTests ................................ Passed 0.22 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (0 ms total) 51: [ PASSED ] 9 tests. 51/94 Test #51: CompatibilityHelpersTests .................... Passed 0.17 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (0 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (428 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (217 ms) 52: [----------] 2 tests from GmxChiTest (722 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (6 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (0 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (0 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (0 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (0 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (0 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (0 ms) 52: [----------] 10 tests from MindistTest (9 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (10 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (743 ms total) 52: [ PASSED ] 31 tests. 52/94 Test #52: GmxAnaTest ................................... Passed 1.01 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 257 tests from 16 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 53: [----------] 4 tests from GenconfTest (1 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to -1208059029 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (194 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to -135830537 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (187 ms) 53: [----------] 2 tests from GenionTest (382 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (0 ms) 53: [----------] 1 test from GenRestrTest (0 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Setting the LD random seed to -27787333 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1736404911 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (4 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to -1157773889 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -35873041 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (0 ms) 53: [----------] 3 tests from GromppDirectiveTest (7 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 53: [----------] 6 tests from InsertMoleculesTest (6 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (1 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (1 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (3 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [----------] 35 tests from GetIrTest (44 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (2 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (11 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (13 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (6 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (43 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 53: [----------] 6 tests from SolvateTest (81 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (0 ms total) 53: 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest (67 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (8 ms total) 53: 53: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -578904066 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2147471855 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1855523 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1083377153 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -440607009 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -402709001 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1830690825 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -135300189 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (0 ms) 53: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (11 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 257 tests from 16 test suites ran. (612 ms total) 53: [ PASSED ] 217 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/94 Test #53: GmxPreprocessTests ........................... Passed 0.89 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (61 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (27 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (59 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (58 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (55 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (823 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (823 ms total) 54: [ PASSED ] 30 tests. 54/94 Test #54: Pdb2gmx1Test ................................. Passed 1.07 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (515 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (29 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (557 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (1072 ms total) 55: [ PASSED ] 40 tests. 55/94 Test #55: Pdb2gmx2Test ................................. Passed 1.27 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (56 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (306 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (64 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (313 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (22 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (22 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (22 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (165 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (16 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (55 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (181 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (47 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (284 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (49 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (562 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (1413 ms total) 56: [ PASSED ] 39 tests. 56/94 Test #56: Pdb2gmx3Test ................................. Passed 1.63 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (56 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (55 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (107 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (99 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (1 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (54 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (68 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (111 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (1 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (101 ms) 57: [----------] 10 tests from AutocorrTest (660 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (22 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (1 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (1 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (3 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (22 ms) 57: [----------] 10 tests from ExpfitTest (55 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (718 ms total) 57: [ PASSED ] 21 tests. 57/94 Test #57: CorrelationsTest ............................. Passed 0.81 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 58: [----------] 6 tests from AverageModuleTest (2 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from BinAverageModuleTest (1 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from LifetimeModuleTest (0 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (14 ms total) 58: [ PASSED ] 69 tests. 58/94 Test #58: AnalysisDataUnitTests ........................ Passed 0.24 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (1 ms) 59: [----------] 1 test from OutputSelectorDeathTest (1 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (5 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (0 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 59: [----------] 5 tests from SetAtomsTest (4 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (5 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (3 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (4 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (8 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (2 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (43 ms total) 59: [ PASSED ] 67 tests. 59/94 Test #59: CoordinateIOTests ............................ Passed 0.14 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 60: [----------] 11 tests from AngleModuleTest (16 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (0 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (0 ms) 60: [----------] 5 tests from ClustsizeTest (5 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (9 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (17 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (4 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (8 ms) 60: [----------] 6 tests from DistanceModuleTest (23 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (3 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (44 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (47 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (92 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (2 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -1692012593 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (15 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to 2111307767 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (15 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -103415827 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (14 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -842739844 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (14 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 2134228267 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (12 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -13649053 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (14 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 1904189383 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (14 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -17322039 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (14 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -23617674 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (17 ms) 60: [----------] 13 tests from MsdModuleTest (141 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 60: [----------] 9 tests from PairDistanceModuleTest (12 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (16 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (11 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 60: [----------] 5 tests from RdfModuleTest (56 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (5 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (4 ms) 60: [----------] 5 tests from SasaModuleTest (21 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (2 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (2 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (2 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 60: [----------] 8 tests from SelectModuleTest (14 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 60: [----------] 10 tests from SurfaceAreaTest (5 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to 2146300975 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (189 ms) 60: [----------] 4 tests from TopologyInformation (191 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (2 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 60: [----------] 4 tests from TrajectoryModuleTest (6 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (2133 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (3 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (3 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (3 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (11 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (21 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (8 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (10 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (17 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (55 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (46 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (58 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (56 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (156 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (49 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (58 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (70 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (52 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (46 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (46 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (58 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (55 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (48 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (43 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (44 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (51 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (45 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (110 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (43 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (64 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (44 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (44 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (55 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (58 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (53 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (43 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (47 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (50 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (49 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (48 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (44 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (3806 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (5 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (175 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (37 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (226 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (6790 ms total) 60: [ PASSED ] 393 tests. 60/94 Test #60: TrajectoryAnalysisUnitTests .................. Passed 6.88 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (4 ms) 61: [----------] 1 test from DhdlTest (5 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (7 ms) 61: [----------] 1 test from OriresTest (7 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 61: [----------] 5 tests from EnergyTest (5 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (145 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (102 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (112 ms) 61: [----------] 3 tests from ViscosityTest (360 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (379 ms total) 61: [ PASSED ] 12 tests. 61/94 Test #61: EnergyAnalysisUnitTests ...................... Passed 0.46 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -575681869 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = -575681869 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 46382 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 62: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 62: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 62: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 62: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 62: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 62: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 62: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 62: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 62: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 62: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 62: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 62: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 62: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 62: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 62: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 62: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 62: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 62: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 62: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 62: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 62: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 62: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 62: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 62: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 62: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 62: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 62: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 62: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 62: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 62: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 62: v (156x3): 62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (5 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 62: [----------] 2 tests from DumpTest (5 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 62: [----------] 3 tests from HelpwritingTest (0 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (1 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (0 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (0 ms) 62: [----------] 7 tests from GmxMakeNdx (4 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to 1070006262 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 62: [----------] 4 tests from ReportMethodsTest (0 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -1090816001 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (179 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -176164865 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (170 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -134766611 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (176 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to 1929116524 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (177 ms) 62: [----------] 4 tests from ConvertTprTest (703 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -11632653 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (188 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (188 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (4 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (10 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (1288 ms total) 62: [ PASSED ] 63 tests. 62/94 Test #62: ToolUnitTests ................................ Passed 1.38 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Setting the LD random seed to 1073741291 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (176 ms) 63: [----------] 1 test from ConvertTprTest (176 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Setting the LD random seed to -1191708686 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (171 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (171 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (347 ms total) 63: [ PASSED ] 2 tests. 63/94 Test #63: ToolWithLeaksUnitTests ....................... Passed 0.58 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (0 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 64: [----------] 1 test from StructureIOTest (0 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (0 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (0 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (0 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 64: [----------] 4 tests from MatioTest (1 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 64: [----------] 4 tests from MrcDensityMap (0 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (0 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (4 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (4 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (11 ms total) 64: [ PASSED ] 421 tests. 64/94 Test #64: FileIOTests .................................. Passed 0.10 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (0 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 65: [----------] 11 tests from IndexMapTest (1 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (21 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (51 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 65: [----------] 13 tests from PositionCalculationTest (1 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 65: [----------] 33 tests from SelectionCollectionTest (7 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (3 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (33 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 65: [----------] 17 tests from SelectionOptionTest (3 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 65: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (103 ms total) 65: [ PASSED ] 201 tests. 65/94 Test #65: SelectionUnitTests ........................... Passed 0.18 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (6 ms) 66: [----------] 1 test from MdrunTest (6 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -503455762 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.002 195.2 66: (ns/day) (hour/ns) 66: Performance: 98.128 0.245 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (20 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -201343489 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.0 66: (ns/day) (hour/ns) 66: Performance: 12.072 1.988 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (18 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1073783049 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 186.3 66: (ns/day) (hour/ns) 66: Performance: 319.848 0.075 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (9 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (48 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 190.8 66: (ns/day) (hour/ns) 66: Performance: 2063.159 0.012 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (13 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 195.6 66: (ns/day) (hour/ns) 66: Performance: 1413.304 0.017 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (5 ms) 66: [----------] 2 tests from Argon12/OutputFiles (19 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 1869610751 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.005 0.002 196.6 66: (ns/day) (hour/ns) 66: Performance: 242.980 0.099 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (16 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -172528386 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.002 195.3 66: (ns/day) (hour/ns) 66: Performance: 314.534 0.076 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (30 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 2125191133 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 193.6 66: (ns/day) (hour/ns) 66: Performance: 426.052 0.056 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (31 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (78 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 1071093375 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.6 66: (ns/day) (hour/ns) 66: Performance: 333.486 0.072 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (19 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -2030649893 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.5 66: (ns/day) (hour/ns) 66: Performance: 363.114 0.066 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (16 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -138184745 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.001 189.3 66: (ns/day) (hour/ns) 66: Performance: 366.666 0.065 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (15 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (51 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (226 ms total) 66: [ PASSED ] 12 tests. 66/94 Test #66: MdrunOutputTests ............................. Passed 0.33 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1630571797 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (12 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.8207725e+03 67: Maximum force = 7.3954834e+03 on atom 2 67: Norm of force = 2.7825089e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2046746365 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (143 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.0954996e+04 67: Maximum force = 7.4724795e+03 on atom 2 67: Norm of force = 2.7758003e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1278218401 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (24 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1352667155 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (4 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.7138664e+04 67: Maximum force = 6.7827656e+03 on atom 2 67: Norm of force = 1.9608866e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2113929179 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (7 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -436249115 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.003 0.001 194.7 67: (ns/day) (hour/ns) 67: Performance: 178.751 0.134 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 188.9 67: (ns/day) (hour/ns) 67: Performance: 777.656 0.031 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (23 ms) 67: [----------] 9 tests from DensityFittingTest (215 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 22 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 182.9 67: (ns/day) (hour/ns) 67: Performance: 461.641 0.052 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1375731749 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (15 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 23 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 184.8 67: (ns/day) (hour/ns) 67: Performance: 501.922 0.048 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -277350529 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (4 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 22 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 184.2 67: (ns/day) (hour/ns) 67: Performance: 439.258 0.055 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1568652099 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (15 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 18 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 188.2 67: (ns/day) (hour/ns) 67: Performance: 330.044 0.073 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1275134700 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (20 ms) 67: [----------] 4 tests from MimicTest (56 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 43181. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -138872897 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 188.0 67: (ns/day) (hour/ns) 67: Performance: 732.837 0.033 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (91 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 42803. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.1977061e+03 67: Maximum force = 1.7794875e+04 on atom 9 67: Norm of force = 7.8732895e+03 67: Setting the LD random seed to -275777029 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (267 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (359 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (648 ms total) 67: [ PASSED ] 15 tests. 67/94 Test #67: MdrunModulesTests ............................ Passed 0.90 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to 1475862527 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1149304867 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -100681478 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to -704708609 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -404142145 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to -50865282 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) 68: [----------] 9 tests from GromppTest (18 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -37832713 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 194.2 68: (ns/day) (hour/ns) 68: Performance: 188.515 0.127 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 187.6 68: (ns/day) (hour/ns) 68: Performance: 475.575 0.050 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (50 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 15: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to -739051795 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 199.3 68: (ns/day) (hour/ns) 68: Performance: 576.079 0.042 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 102 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 188.5 68: (ns/day) (hour/ns) 68: Performance: 504.484 0.048 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (25 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -310642741 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 190.7 68: (ns/day) (hour/ns) 68: Performance: 254.784 0.094 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 190.3 68: (ns/day) (hour/ns) 68: Performance: 536.077 0.045 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 6 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 190.3 68: (ns/day) (hour/ns) 68: Performance: 572.794 0.042 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 8 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 191.6 68: (ns/day) (hour/ns) 68: Performance: 553.264 0.043 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 25 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.000 0.000 168.8 68: (ns/day) (hour/ns) 68: Performance: 570.690 0.042 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (45 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 2142752693 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 185.8 68: (ns/day) (hour/ns) 68: Performance: 547.138 0.044 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 199.4 68: (ns/day) (hour/ns) 68: Performance: 20.066 1.196 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (43 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -103386371 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.008 0.004 197.1 68: (ns/day) (hour/ns) 68: Performance: 62.737 0.383 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (52 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -271593800 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 186.7 68: (ns/day) (hour/ns) 68: Performance: 462.033 0.052 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.000 190.1 68: (ns/day) (hour/ns) 68: Performance: 545.217 0.044 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (60 ms) 68: [----------] 6 tests from MdrunTerminationTest (278 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.0 68: (ns/day) (hour/ns) 68: Performance: 2116.315 0.011 68: trr version: GMX_trn_file (single precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (11 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 194.4 68: (ns/day) (hour/ns) 68: Performance: 1567.581 0.015 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (16 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (28 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.016 199.2 68: (ns/day) (hour/ns) 68: Performance: 92.973 0.258 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.5 68: (ns/day) (hour/ns) 68: Performance: 1380.233 0.017 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 191.3 68: (ns/day) (hour/ns) 68: Performance: 815.373 0.029 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (38 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.008 198.2 68: (ns/day) (hour/ns) 68: Performance: 188.230 0.128 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.3 68: (ns/day) (hour/ns) 68: Performance: 1369.799 0.018 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 199.3 68: (ns/day) (hour/ns) 68: Performance: 45.102 0.532 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (40 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 194.8 68: (ns/day) (hour/ns) 68: Performance: 1592.708 0.015 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 193.2 68: (ns/day) (hour/ns) 68: Performance: 950.595 0.025 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.0 68: (ns/day) (hour/ns) 68: Performance: 1000.151 0.024 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (47 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 194.5 68: (ns/day) (hour/ns) 68: Performance: 1625.915 0.015 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 194.3 68: (ns/day) (hour/ns) 68: Performance: 1073.565 0.022 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.3 68: (ns/day) (hour/ns) 68: Performance: 1025.304 0.023 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (21 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 199.5 68: (ns/day) (hour/ns) 68: Performance: 62.005 0.387 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.3 68: (ns/day) (hour/ns) 68: Performance: 1342.177 0.018 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.0 68: (ns/day) (hour/ns) 68: Performance: 1315.117 0.018 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (45 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.2 68: (ns/day) (hour/ns) 68: Performance: 2157.071 0.011 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.6 68: (ns/day) (hour/ns) 68: Performance: 1455.373 0.016 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.6 68: (ns/day) (hour/ns) 68: Performance: 1324.732 0.018 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (26 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.008 198.5 68: (ns/day) (hour/ns) 68: Performance: 189.056 0.127 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.4 68: (ns/day) (hour/ns) 68: Performance: 1355.002 0.018 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.3 68: (ns/day) (hour/ns) 68: Performance: 1197.756 0.020 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (35 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.5 68: (ns/day) (hour/ns) 68: Performance: 2086.215 0.012 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.0 68: (ns/day) (hour/ns) 68: Performance: 1407.028 0.017 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.9 68: (ns/day) (hour/ns) 68: Performance: 1327.428 0.018 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (16 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.9 68: (ns/day) (hour/ns) 68: Performance: 2204.148 0.011 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.0 68: (ns/day) (hour/ns) 68: Performance: 1441.224 0.017 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.8 68: (ns/day) (hour/ns) 68: Performance: 1298.364 0.018 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (11 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.7 68: (ns/day) (hour/ns) 68: Performance: 2205.726 0.011 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 188.7 68: (ns/day) (hour/ns) 68: Performance: 1392.609 0.017 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.4 68: (ns/day) (hour/ns) 68: Performance: 1260.723 0.019 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (12 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 195.3 68: (ns/day) (hour/ns) 68: Performance: 1611.455 0.015 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.5 68: (ns/day) (hour/ns) 68: Performance: 57.295 0.419 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.021 199.6 68: (ns/day) (hour/ns) 68: Performance: 36.504 0.657 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (47 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 199.7 68: (ns/day) (hour/ns) 68: Performance: 86.421 0.278 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 83 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.116 0.058 199.9 68: (ns/day) (hour/ns) 68: Performance: 13.425 1.788 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 44 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 199.5 68: (ns/day) (hour/ns) 68: Performance: 41.970 0.572 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (143 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.008 198.4 68: (ns/day) (hour/ns) 68: Performance: 185.789 0.129 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.014 199.2 68: (ns/day) (hour/ns) 68: Performance: 53.728 0.447 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.010 198.9 68: (ns/day) (hour/ns) 68: Performance: 74.719 0.321 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (59 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.008 198.7 68: (ns/day) (hour/ns) 68: Performance: 185.236 0.130 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.009 0.004 197.4 68: (ns/day) (hour/ns) 68: Performance: 178.058 0.135 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.540 1.228 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (70 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.167 0.083 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.614 1.363 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.086 0.043 199.8 68: (ns/day) (hour/ns) 68: Performance: 18.083 1.327 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.4 68: (ns/day) (hour/ns) 68: Performance: 1185.135 0.020 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (148 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.005 0.003 196.1 68: (ns/day) (hour/ns) 68: Performance: 581.188 0.041 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.094 0.047 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.452 1.459 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.106 0.053 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.680 1.635 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (120 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.444 0.222 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.614 3.628 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.277 0.138 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.617 4.273 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.279 0.140 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.572 4.307 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (604 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.462 0.231 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.355 3.776 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.224 0.112 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.950 3.453 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.224 0.112 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.951 3.453 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (528 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.494 0.247 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.947 4.035 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.265 0.133 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.859 4.097 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.260 0.130 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.988 4.008 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (564 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.324 0.162 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.065 2.648 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.013 0.006 197.8 68: (ns/day) (hour/ns) 68: Performance: 122.021 0.197 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.765 0.383 200.0 68: (ns/day) (hour/ns) 68: Performance: 2.033 11.806 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (808 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.531 0.265 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.535 4.336 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.241 0.120 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.455 3.718 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.227 0.113 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.861 3.498 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (576 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.008 198.5 68: (ns/day) (hour/ns) 68: Performance: 188.064 0.128 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.251 0.126 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.185 3.880 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.219 0.110 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.089 3.386 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (389 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.369 0.185 200.0 68: (ns/day) (hour/ns) 68: Performance: 7.956 3.016 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 193.0 68: (ns/day) (hour/ns) 68: Performance: 658.222 0.036 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 193.3 68: (ns/day) (hour/ns) 68: Performance: 639.759 0.038 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (269 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 195.8 68: (ns/day) (hour/ns) 68: Performance: 725.715 0.033 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.346 0.173 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.493 5.342 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.347 0.173 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.486 5.350 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (467 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5096 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.078 0.039 199.7 68: (ns/day) (hour/ns) 68: Performance: 37.833 0.634 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 189.5 68: (ns/day) (hour/ns) 68: Performance: 643.165 0.037 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 190.6 68: (ns/day) (hour/ns) 68: Performance: 742.260 0.032 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (69 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 199.1 68: (ns/day) (hour/ns) 68: Performance: 80.705 0.297 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 192.4 68: (ns/day) (hour/ns) 68: Performance: 532.401 0.045 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.1 68: (ns/day) (hour/ns) 68: Performance: 88.146 0.272 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (65 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 196.2 68: (ns/day) (hour/ns) 68: Performance: 818.466 0.029 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 196.0 68: (ns/day) (hour/ns) 68: Performance: 415.477 0.058 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 189.7 68: (ns/day) (hour/ns) 68: Performance: 513.701 0.047 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (61 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 196.2 68: (ns/day) (hour/ns) 68: Performance: 828.037 0.029 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.019 0.010 199.3 68: (ns/day) (hour/ns) 68: Performance: 79.884 0.300 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.010 0.005 196.8 68: (ns/day) (hour/ns) 68: Performance: 153.844 0.156 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (47 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.187 0.094 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.692 1.529 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.104 0.052 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.979 1.602 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.104 0.052 199.7 68: (ns/day) (hour/ns) 68: Performance: 14.944 1.606 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (257 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.182 0.091 199.9 68: (ns/day) (hour/ns) 68: Performance: 16.173 1.484 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.104 0.052 199.7 68: (ns/day) (hour/ns) 68: Performance: 14.937 1.607 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.048 199.7 68: (ns/day) (hour/ns) 68: Performance: 16.086 1.492 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (329 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.227 0.114 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.928 1.856 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.126 0.063 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.367 1.941 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.6 68: (ns/day) (hour/ns) 68: Performance: 21.439 1.119 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (265 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.014 198.9 68: (ns/day) (hour/ns) 68: Performance: 102.041 0.235 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.006 0.003 194.6 68: (ns/day) (hour/ns) 68: Performance: 259.136 0.093 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.819 0.909 200.0 68: (ns/day) (hour/ns) 68: Performance: 0.855 28.070 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1258 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2354 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.7 68: (ns/day) (hour/ns) 68: Performance: 1945.860 0.012 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.8 68: (ns/day) (hour/ns) 68: Performance: 1341.074 0.018 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 190.8 68: (ns/day) (hour/ns) 68: Performance: 1239.639 0.019 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (11 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 192.0 68: (ns/day) (hour/ns) 68: Performance: 2015.901 0.012 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 189.9 68: (ns/day) (hour/ns) 68: Performance: 1343.836 0.018 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 192.3 68: (ns/day) (hour/ns) 68: Performance: 930.791 0.026 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (15 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.849 0.425 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.460 6.937 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 188.7 68: (ns/day) (hour/ns) 68: Performance: 635.025 0.038 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 188.5 68: (ns/day) (hour/ns) 68: Performance: 597.233 0.040 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (440 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 191.1 68: (ns/day) (hour/ns) 68: Performance: 891.290 0.027 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 188.3 68: (ns/day) (hour/ns) 68: Performance: 586.388 0.041 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 191.9 68: (ns/day) (hour/ns) 68: Performance: 360.585 0.067 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (28 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 196.3 68: (ns/day) (hour/ns) 68: Performance: 669.994 0.036 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 194.9 68: (ns/day) (hour/ns) 68: Performance: 482.112 0.050 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 192.2 68: (ns/day) (hour/ns) 68: Performance: 386.112 0.062 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (27 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 194.6 68: (ns/day) (hour/ns) 68: Performance: 824.932 0.029 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 193.9 68: (ns/day) (hour/ns) 68: Performance: 578.586 0.041 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.002 192.4 68: (ns/day) (hour/ns) 68: Performance: 388.458 0.062 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (27 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.007 0.004 196.3 68: (ns/day) (hour/ns) 68: Performance: 395.189 0.061 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.095 0.047 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.415 1.462 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.7 68: (ns/day) (hour/ns) 68: Performance: 16.112 1.490 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1152 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.155 0.077 199.9 68: (ns/day) (hour/ns) 68: Performance: 18.975 1.265 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.100 0.050 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.608 1.538 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.090 0.045 199.7 68: (ns/day) (hour/ns) 68: Performance: 17.330 1.385 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (187 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1891 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.8 68: (ns/day) (hour/ns) 68: Performance: 22.514 1.066 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 24 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.189 0.094 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.230 2.916 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.246 0.123 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.312 3.802 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (304 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.147 0.074 199.9 68: (ns/day) (hour/ns) 68: Performance: 19.979 1.201 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.086 0.043 199.8 68: (ns/day) (hour/ns) 68: Performance: 18.115 1.325 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.085 0.042 199.7 68: (ns/day) (hour/ns) 68: Performance: 18.369 1.307 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (174 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (478 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.999 1.000 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.210 1.188 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.358 1.073 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (156 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.057 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.559 0.939 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.002 193.8 68: (ns/day) (hour/ns) 68: Performance: 506.836 0.047 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.110 0.055 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.070 1.706 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (182 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.083 0.041 199.7 68: (ns/day) (hour/ns) 68: Performance: 35.466 0.677 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.7 68: (ns/day) (hour/ns) 68: Performance: 16.214 1.480 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 34 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.328 0.164 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.740 5.063 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (307 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 199.4 68: (ns/day) (hour/ns) 68: Performance: 72.671 0.330 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.008 0.004 196.8 68: (ns/day) (hour/ns) 68: Performance: 196.665 0.122 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 58 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 199.6 68: (ns/day) (hour/ns) 68: Performance: 27.759 0.865 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (160 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 41 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.020 199.6 68: (ns/day) (hour/ns) 68: Performance: 71.651 0.335 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 40 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.400 0.200 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.886 6.177 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 43 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.296 0.148 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.243 4.577 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (464 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 78 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.8 68: (ns/day) (hour/ns) 68: Performance: 40.576 0.591 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 46 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.089 0.044 199.8 68: (ns/day) (hour/ns) 68: Performance: 17.543 1.368 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 62 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.320 0.160 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.855 4.943 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (320 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 195.4 68: (ns/day) (hour/ns) 68: Performance: 1030.372 0.023 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 194.1 68: (ns/day) (hour/ns) 68: Performance: 912.305 0.026 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 189.3 68: (ns/day) (hour/ns) 68: Performance: 823.817 0.029 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (17 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1609 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 194.9 68: (ns/day) (hour/ns) 68: Performance: 1092.885 0.022 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 193.8 68: (ns/day) (hour/ns) 68: Performance: 541.776 0.044 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 189.7 68: (ns/day) (hour/ns) 68: Performance: 717.916 0.033 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (21 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (21 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 188.7 68: (ns/day) (hour/ns) 68: Performance: 1829.155 0.013 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 187.9 68: (ns/day) (hour/ns) 68: Performance: 1164.818 0.021 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 188.6 68: (ns/day) (hour/ns) 68: Performance: 1110.106 0.022 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (18 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 194.1 68: (ns/day) (hour/ns) 68: Performance: 1430.700 0.017 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 192.8 68: (ns/day) (hour/ns) 68: Performance: 877.452 0.027 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 188.8 68: (ns/day) (hour/ns) 68: Performance: 814.558 0.029 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (23 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (41 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to -1091567626 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -1744872195 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.008 197.3 68: (ns/day) (hour/ns) 68: Performance: 189.516 0.127 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.013 0.007 197.0 68: (ns/day) (hour/ns) 68: Performance: 118.548 0.202 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 189.1 68: (ns/day) (hour/ns) 68: Performance: 627.451 0.038 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (56 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to -689025 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -672737081 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.224 0.112 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.132 1.828 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.117 0.059 199.7 68: (ns/day) (hour/ns) 68: Performance: 13.226 1.815 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.113 0.057 199.7 68: (ns/day) (hour/ns) 68: Performance: 13.684 1.754 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (276 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (333 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.245 0.122 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.993 2.001 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.388 2.107 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.958 2.007 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (300 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (300 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1367627274 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 199.3 68: (ns/day) (hour/ns) 68: Performance: 13.021 1.843 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (23 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1209665570 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 199.6 68: (ns/day) (hour/ns) 68: Performance: 9.162 2.619 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (26 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -536936689 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 199.5 68: (ns/day) (hour/ns) 68: Performance: 8.989 2.670 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (31 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (80 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (12617 ms total) 68: [ PASSED ] 76 tests. 68/94 Test #68: MdrunIOTests ................................. Passed 12.79 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Setting the LD random seed to 1602181631 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: NOTE: 30 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.337 0.168 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.697 3.118 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.261 0.131 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.911 2.422 69: [ OK ] CompelTest.SwapCanRun (547 ms) 69: [----------] 1 test from CompelTest (547 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Setting the LD random seed to -51381538 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.3 69: (ns/day) (hour/ns) 69: Performance: 15.674 1.531 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: [ OK ] BondedInteractionsTest.NormalBondWorks (10 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: Setting the LD random seed to -1350730297 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.4 69: (ns/day) (hour/ns) 69: Performance: 15.606 1.538 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (11 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: Setting the LD random seed to -52863010 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 53 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.3 69: (ns/day) (hour/ns) 69: Performance: 15.513 1.547 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (10 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: Setting the LD random seed to 438792028 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.2 69: (ns/day) (hour/ns) 69: Performance: 15.626 1.536 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (11 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: Setting the LD random seed to -1644707874 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 50 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.012 0.006 199.2 69: (ns/day) (hour/ns) 69: Performance: 14.750 1.627 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (11 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: Setting the LD random seed to -167840897 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.3 69: (ns/day) (hour/ns) 69: Performance: 15.627 1.536 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (11 ms) 69: [----------] 6 tests from BondedInteractionsTest (67 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: Setting the LD random seed to -42599075 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to -151683090 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: 41 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.014 0.007 199.0 69: (ns/day) (hour/ns) 69: Performance: 24.296 0.988 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (14 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: Setting the LD random seed to -273718275 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.23 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: NOTE: 7 % of the run time was spent in domain decomposition, 69: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.331 0.166 199.9 69: (ns/day) (hour/ns) 69: Performance: 21.919 1.095 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1582 ms) 69: [----------] 2 tests from BoxDeformationTest (1596 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Setting the LD random seed to -33653298 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: This run will generate roughly 1 Mb of data 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.389 0.195 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.762 2.459 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (414 ms) 69: [----------] 1 test from PositionRestraintCommTest (414 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -33554693 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.002 194.0 69: (ns/day) (hour/ns) 69: Performance: 269.955 0.089 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -1082146913 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.020 0.010 198.5 69: (ns/day) (hour/ns) 69: Performance: 43.894 0.547 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (25104 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: Setting the LD random seed to 2080374718 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.018 0.009 198.4 69: (ns/day) (hour/ns) 69: Performance: 47.016 0.510 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -114758 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.019 0.010 198.5 69: (ns/day) (hour/ns) 69: Performance: 43.999 0.545 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (51 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (25156 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: Setting the LD random seed to -411713572 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.021 0.011 198.5 69: (ns/day) (hour/ns) 69: Performance: 40.808 0.588 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Setting the LD random seed to 1861205247 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 187.8 69: (ns/day) (hour/ns) 69: Performance: 684.526 0.035 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (20 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (20 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (9 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 189.7 69: (ns/day) (hour/ns) 69: Performance: 996.179 0.024 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.017 0.009 198.4 69: (ns/day) (hour/ns) 69: Performance: 89.668 0.268 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (17 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.008 0.004 196.6 69: (ns/day) (hour/ns) 69: Performance: 190.619 0.126 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (20 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.7 69: (ns/day) (hour/ns) 69: Performance: 71.022 0.338 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (19 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.023 0.011 198.8 69: (ns/day) (hour/ns) 69: Performance: 68.682 0.349 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (20 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 190.8 69: (ns/day) (hour/ns) 69: Performance: 972.708 0.025 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (21 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 190.4 69: (ns/day) (hour/ns) 69: Performance: 938.559 0.026 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (12 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 189.9 69: (ns/day) (hour/ns) 69: Performance: 863.742 0.028 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (58 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 190.0 69: (ns/day) (hour/ns) 69: Performance: 1017.626 0.024 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (33 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.016 0.008 198.4 69: (ns/day) (hour/ns) 69: Performance: 99.139 0.242 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (45 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 189.0 69: (ns/day) (hour/ns) 69: Performance: 942.355 0.025 69: 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (44 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (303 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -71438745 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 187.9 69: (ns/day) (hour/ns) 69: Performance: 2660.270 0.009 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (7 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -2261041 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.019 199.3 69: (ns/day) (hour/ns) 69: Performance: 81.001 0.296 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (23 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -1074029058 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.032 0.016 199.2 69: (ns/day) (hour/ns) 69: Performance: 97.812 0.245 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (19 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -545783842 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 188.1 69: (ns/day) (hour/ns) 69: Performance: 2403.457 0.010 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (16 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (67 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (28208 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/94 Test #69: MdrunTestsOneRank ............................ Passed 28.64 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Setting the LD random seed to -1216349509 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: 70: This run will generate roughly 1 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 1.4%. 70: The balanceable part of the MD step is 17%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.2%. 70: 70: 70: NOTE: 28 % of the run time was spent in domain decomposition, 70: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.216 0.304 399.9 70: (ns/day) (hour/ns) 70: Performance: 4.262 5.631 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.496 0.124 399.6 70: (ns/day) (hour/ns) 70: Performance: 10.451 2.296 70: [ OK ] CompelTest.SwapCanRun (961 ms) 70: [----------] 1 test from CompelTest (961 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: Setting the LD random seed to 1171190926 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 48 % of the run time was spent in domain decomposition, 70: 34 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.060 0.015 399.3 70: (ns/day) (hour/ns) 70: Performance: 5.788 4.147 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: [ OK ] BondedInteractionsTest.NormalBondWorks (30 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: Setting the LD random seed to -69713 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 40 % of the run time was spent in domain decomposition, 70: 40 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.073 0.018 399.4 70: (ns/day) (hour/ns) 70: Performance: 4.741 5.062 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (30 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: Setting the LD random seed to -1245708811 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 15 % of the run time was spent in domain decomposition, 70: 47 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 36 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.211 0.053 399.7 70: (ns/day) (hour/ns) 70: Performance: 1.633 14.696 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (64 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: Setting the LD random seed to -1107298733 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.010 0.002 396.8 70: (ns/day) (hour/ns) 70: Performance: 34.629 0.693 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (56 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: Setting the LD random seed to 2074985978 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 52 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.245 0.061 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.409 17.031 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (159 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: Setting the LD random seed to -671351873 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 64 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.203 0.051 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.698 14.137 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (75 ms) 70: [----------] 6 tests from BondedInteractionsTest (417 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: Setting the LD random seed to -30409265 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to -163953 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 70 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.210 0.056 374.2 70: (ns/day) (hour/ns) 70: Performance: 3.084 7.782 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (114 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: Setting the LD random seed to -211256329 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 2 NOTEs 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.23 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 3.3%. 70: The balanceable part of the MD step is 25%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.8%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.475 0.619 399.9 70: (ns/day) (hour/ns) 70: Performance: 5.865 4.092 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2079 ms) 70: [----------] 2 tests from BoxDeformationTest (2194 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: Setting the LD random seed to -272629793 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 5 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.762 0.191 399.8 70: (ns/day) (hour/ns) 70: Performance: 9.967 2.408 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (457 ms) 70: [----------] 1 test from PositionRestraintCommTest (457 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to -38797575 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.678 0.170 399.8 70: (ns/day) (hour/ns) 70: Performance: 2.548 9.418 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to 2097119159 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 16 % of the run time was spent in domain decomposition, 70: 1 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.733 0.183 399.8 70: (ns/day) (hour/ns) 70: Performance: 2.357 10.182 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (26356 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: Setting the LD random seed to -19483201 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 1 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.848 0.212 399.9 70: (ns/day) (hour/ns) 70: Performance: 2.036 11.786 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to 532408303 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 9 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.313 0.078 399.6 70: (ns/day) (hour/ns) 70: Performance: 5.518 4.350 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (432 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (26788 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Setting the LD random seed to 2105269572 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.136 0.034 399.2 70: (ns/day) (hour/ns) 70: Performance: 12.702 1.890 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Setting the LD random seed to 2147260397 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.533 0.133 399.8 70: (ns/day) (hour/ns) 70: Performance: 3.237 7.414 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (205 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (205 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 41.2%. 70: The balanceable part of the MD step is 35%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 14.6%. 70: 70: NOTE: 14.6 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 26 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.843 0.211 399.2 70: (ns/day) (hour/ns) 70: Performance: 3.682 6.519 70: 70: 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (272 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 25.5%. 70: The balanceable part of the MD step is 44%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 11.3%. 70: 70: NOTE: 11.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 15 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.859 0.215 398.9 70: (ns/day) (hour/ns) 70: Performance: 3.609 6.650 70: 70: 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (288 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.6%. 70: The balanceable part of the MD step is 4%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.3%. 70: 70: 70: NOTE: 40 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.176 0.060 293.7 70: (ns/day) (hour/ns) 70: Performance: 12.970 1.850 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (232 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 5.4%. 70: The balanceable part of the MD step is 1%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 67 % of the run time was spent in domain decomposition, 70: 0 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 25 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.120 0.030 398.7 70: (ns/day) (hour/ns) 70: Performance: 25.793 0.930 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (103 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 4.3%. 70: The balanceable part of the MD step is 50%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.1%. 70: 70: 70: NOTE: 18 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.039 0.016 249.2 70: (ns/day) (hour/ns) 70: Performance: 49.350 0.486 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (39 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.650 0.163 398.8 70: (ns/day) (hour/ns) 70: Performance: 4.770 5.032 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (284 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 31 % of the run time was spent in domain decomposition, 70: 0 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.727 0.182 399.4 70: (ns/day) (hour/ns) 70: Performance: 4.272 5.617 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (209 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.387 0.097 399.7 70: (ns/day) (hour/ns) 70: Performance: 8.025 2.991 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (138 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.327 0.082 398.6 70: (ns/day) (hour/ns) 70: Performance: 9.489 2.529 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (126 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 7 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.283 0.071 398.4 70: (ns/day) (hour/ns) 70: Performance: 10.961 2.190 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (130 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 7 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.256 0.064 398.2 70: (ns/day) (hour/ns) 70: Performance: 12.093 1.985 70: 70: 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (111 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1939 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 2146432767 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 54%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 21 % of the run time was spent in domain decomposition, 70: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.264 0.066 399.6 70: (ns/day) (hour/ns) 70: Performance: 23.503 1.021 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (80 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -8800257 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 58%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 25 % of the run time was spent in domain decomposition, 70: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.233 0.058 399.5 70: (ns/day) (hour/ns) 70: Performance: 26.662 0.900 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (71 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -573652098 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.1%. 70: The balanceable part of the MD step is 62%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 21 % of the run time was spent in domain decomposition, 70: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.275 0.069 399.6 70: (ns/day) (hour/ns) 70: Performance: 22.579 1.063 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (82 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 1065153789 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 62%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 21 % of the run time was spent in domain decomposition, 70: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.275 0.069 399.6 70: (ns/day) (hour/ns) 70: Performance: 22.572 1.063 70: 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (82 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (317 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (33339 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/94 Test #70: MdrunTestsTwoRanks ........................... Passed 33.84 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to -842809859 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.320 0.160 199.9 71: (ns/day) (hour/ns) 71: Performance: 217.289 0.110 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (195 ms) 71: [----------] 1 test from DispersionCorrectionTest (195 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to -436340285 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.016 0.008 198.1 71: (ns/day) (hour/ns) 71: Performance: 237.943 0.101 71: [ OK ] OriresTest.OriresCanRun (331 ms) 71: [----------] 1 test from OriresTest (331 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to 2130705015 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.022 0.011 198.7 71: (ns/day) (hour/ns) 71: Performance: 402.892 0.060 71: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (42296 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -42237955 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.412 0.206 200.0 71: (ns/day) (hour/ns) 71: Performance: 22.008 1.091 71: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (17337 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (59633 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (60174 ms total) 71: [ PASSED ] 5 tests. 71/94 Test #71: MdrunSingleRankAlgorithmsTests ............... Passed 60.39 sec test 72 Start 72: Minimize1RankTests 72: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.7990997e+01 72: Maximum force = 1.8629692e+02 on atom 13 72: Norm of force = 8.7721836e+01 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (171 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.5862350e+01 72: Maximum force = 4.2726685e+02 on atom 13 72: Norm of force = 1.8452681e+02 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (171 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: This run will generate roughly 0 Mb of data 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1937723e+02 72: Maximum force = 9.9988691e+03 on atom 9 72: Norm of force = 4.6167015e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (92 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: 72: turning H bonds into constraints... 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5174414e+02 72: Maximum force = 7.4208760e+03 on atom 9 72: Norm of force = 3.5692977e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (94 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: This run will generate roughly 0 Mb of data 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.5698444e+02 72: Maximum force = 4.5702216e+02 on atom 17 72: Norm of force = 1.8327095e+02 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (76 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06799e+03 on atom 28 72: F-Norm = 4.26914e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.6941235e+02 72: Maximum force = 2.1838167e+02 on atom 17 72: Norm of force = 7.9235206e+01 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (112 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (719 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.7425687e-01 72: Maximum force = 4.0132279e+00 on atom 1 72: Norm of force = 1.6383933e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (10 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (12 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1939673e+02 72: Maximum force = 9.9704229e+03 on atom 9 72: Norm of force = 4.6227534e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (82 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: This run will generate roughly 0 Mb of data 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5625757e+02 72: Maximum force = 7.5018237e+03 on atom 9 72: Norm of force = 3.6139019e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (85 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: Double precision normally gives you higher accuracy, but this is often not 72: needed for preparing to run molecular dynamics. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.6111578e+02 72: Maximum force = 1.2685402e+04 on atom 10 72: Norm of force = 6.0643536e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (82 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (286 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (1013 ms total) 72: [ PASSED ] 12 tests. 72/94 Test #72: Minimize1RankTests ........................... Passed 1.50 sec test 73 Start 73: Minimize2RankTests 73: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.7990952e+01 73: Maximum force = 1.8629709e+02 on atom 13 73: Norm of force = 8.7721970e+01 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (313 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.5862202e+01 73: Maximum force = 4.2727243e+02 on atom 13 73: Norm of force = 1.8452909e+02 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (322 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: This run will generate roughly 0 Mb of data 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1937720e+02 73: Maximum force = 9.9988691e+03 on atom 9 73: Norm of force = 4.6167015e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (137 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: This run will generate roughly 0 Mb of data 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5174358e+02 73: Maximum force = 7.4208833e+03 on atom 9 73: Norm of force = 3.5692986e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (154 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.5698444e+02 73: Maximum force = 4.5702219e+02 on atom 17 73: Norm of force = 1.8327095e+02 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (123 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06799e+03 on atom 28 73: F-Norm = 4.26914e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.6941229e+02 73: Maximum force = 2.1838167e+02 on atom 17 73: Norm of force = 7.9235200e+01 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (233 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1285 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.7425687e-01 73: Maximum force = 4.0132279e+00 on atom 3 73: Norm of force = 1.6383933e+00 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (31 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.9064195e-01 73: Maximum force = 2.5781672e+00 on atom 3 73: Norm of force = 1.0525324e+00 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (36 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1939664e+02 73: Maximum force = 9.9704229e+03 on atom 9 73: Norm of force = 4.6227537e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (133 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5625764e+02 73: Maximum force = 7.5018237e+03 on atom 9 73: Norm of force = 3.6139019e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (157 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (56 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (418 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (1719 ms total) 73: [ PASSED ] 12 tests. 73/94 Test #73: Minimize2RankTests ........................... Passed 2.00 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 46 tests from 3 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: SIMD width: 4 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. 4xM 0.117 0.1166 10.2110 5.4021 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (15 ms) 74: [----------] 1 test from NonbondedBenchTest (15 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.096 0.048 199.7 74: (ns/day) (hour/ns) 74: Performance: 30.675 0.782 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (single precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 80 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.040 0.020 199.7 74: (ns/day) (hour/ns) 74: Performance: 74.088 0.324 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (100 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 73 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.136 0.068 199.9 74: (ns/day) (hour/ns) 74: Performance: 21.541 1.114 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 60 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.041 0.020 199.7 74: (ns/day) (hour/ns) 74: Performance: 72.053 0.333 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (124 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 199.6 74: (ns/day) (hour/ns) 74: Performance: 40.852 0.587 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 44 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 199.2 74: (ns/day) (hour/ns) 74: Performance: 219.402 0.109 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (87 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.043 0.021 199.5 74: (ns/day) (hour/ns) 74: Performance: 68.704 0.349 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 49 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.058 0.029 199.8 74: (ns/day) (hour/ns) 74: Performance: 50.637 0.474 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (72 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.133 0.066 199.9 74: (ns/day) (hour/ns) 74: Performance: 22.091 1.086 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 59 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.042 0.021 199.8 74: (ns/day) (hour/ns) 74: Performance: 70.633 0.340 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (260 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.174 0.087 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.841 1.425 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 59 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.042 0.021 199.7 74: (ns/day) (hour/ns) 74: Performance: 69.799 0.344 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (265 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.141 0.070 199.9 74: (ns/day) (hour/ns) 74: Performance: 20.848 1.151 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 58 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.050 0.025 199.8 74: (ns/day) (hour/ns) 74: Performance: 59.118 0.406 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (266 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.241 0.121 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.189 1.969 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 60 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.041 0.020 199.7 74: (ns/day) (hour/ns) 74: Performance: 71.691 0.335 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (321 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.047 0.024 199.4 74: (ns/day) (hour/ns) 74: Performance: 61.783 0.388 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.034 199.8 74: (ns/day) (hour/ns) 74: Performance: 42.703 0.562 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (119 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.493 0.247 200.0 74: (ns/day) (hour/ns) 74: Performance: 5.954 4.031 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.8 74: (ns/day) (hour/ns) 74: Performance: 45.626 0.526 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (310 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.415 0.207 199.9 74: (ns/day) (hour/ns) 74: Performance: 7.081 3.389 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.039 199.8 74: (ns/day) (hour/ns) 74: Performance: 38.145 0.629 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (340 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.652 0.326 200.0 74: (ns/day) (hour/ns) 74: Performance: 4.501 5.332 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.035 199.8 74: (ns/day) (hour/ns) 74: Performance: 42.479 0.565 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (417 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2689 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.180 0.090 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.265 1.476 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 50.075 0.479 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (140 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.187 0.094 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.672 1.531 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.856 0.481 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (144 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.183 0.091 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.052 1.495 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.905 0.481 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.180 0.090 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.269 1.475 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.3 74: (ns/day) (hour/ns) 74: Performance: 49.860 0.481 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (140 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.183 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.070 1.493 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.581 0.484 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.180 0.090 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.287 1.474 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.983 0.480 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (140 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.090 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.258 1.476 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 50.003 0.480 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.180 0.090 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.265 1.476 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 61 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 199.7 74: (ns/day) (hour/ns) 74: Performance: 43.524 0.551 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (146 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.187 0.094 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.664 1.532 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 61 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 199.7 74: (ns/day) (hour/ns) 74: Performance: 43.602 0.550 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (149 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.203 1.481 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.675 0.483 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (142 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.090 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.236 1.478 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.782 0.482 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.243 0.122 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.067 1.989 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 64 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.011 0.005 198.7 74: (ns/day) (hour/ns) 74: Performance: 274.109 0.088 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (145 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.229 0.115 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.809 1.874 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.726 0.483 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (162 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.168 0.084 199.9 74: (ns/day) (hour/ns) 74: Performance: 17.470 1.374 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 189.9 74: (ns/day) (hour/ns) 74: Performance: 2496.189 0.010 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (100 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.006 198.7 74: (ns/day) (hour/ns) 74: Performance: 232.915 0.103 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 188.8 74: (ns/day) (hour/ns) 74: Performance: 2221.635 0.011 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (19 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 196.1 74: (ns/day) (hour/ns) 74: Performance: 825.706 0.029 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 188.8 74: (ns/day) (hour/ns) 74: Performance: 2126.543 0.011 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (32 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 197.1 74: (ns/day) (hour/ns) 74: Performance: 557.066 0.043 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 190.0 74: (ns/day) (hour/ns) 74: Performance: 2424.476 0.010 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (19 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.002 196.3 74: (ns/day) (hour/ns) 74: Performance: 694.230 0.035 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 58 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 199.7 74: (ns/day) (hour/ns) 74: Performance: 43.362 0.553 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (52 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.010 199.3 74: (ns/day) (hour/ns) 74: Performance: 143.768 0.167 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.008 0.004 197.6 74: (ns/day) (hour/ns) 74: Performance: 374.869 0.064 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (30 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.002 196.6 74: (ns/day) (hour/ns) 74: Performance: 715.766 0.034 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 33 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 192.2 74: (ns/day) (hour/ns) 74: Performance: 2129.483 0.011 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (19 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.034 0.017 199.6 74: (ns/day) (hour/ns) 74: Performance: 87.282 0.275 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.062 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 47.668 0.503 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (63 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.192 0.096 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.263 1.572 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 18 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 185.8 74: (ns/day) (hour/ns) 74: Performance: 2078.473 0.012 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (142 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.096 0.048 199.7 74: (ns/day) (hour/ns) 74: Performance: 30.602 0.784 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 18 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 188.3 74: (ns/day) (hour/ns) 74: Performance: 2163.890 0.011 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (84 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.213 0.106 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.797 1.740 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.063 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 46.447 0.517 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (183 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.213 0.107 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.789 1.741 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 46.174 0.520 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (170 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.156 0.078 199.8 74: (ns/day) (hour/ns) 74: Performance: 18.803 1.276 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.063 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 46.672 0.514 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (139 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.212 0.106 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.863 1.731 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 67 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.078 0.039 199.7 74: (ns/day) (hour/ns) 74: Performance: 37.391 0.642 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.008 198.0 74: (ns/day) (hour/ns) 74: Performance: 185.047 0.130 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.403 0.529 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (66 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 193.6 74: (ns/day) (hour/ns) 74: Performance: 1068.991 0.022 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 189.5 74: (ns/day) (hour/ns) 74: Performance: 2019.867 0.012 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (49 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.087 0.044 199.7 74: (ns/day) (hour/ns) 74: Performance: 33.713 0.712 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.911 0.523 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (108 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.240 0.120 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.234 1.962 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 189.9 74: (ns/day) (hour/ns) 74: Performance: 2025.845 0.012 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (183 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.008 196.5 74: (ns/day) (hour/ns) 74: Performance: 178.687 0.134 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 46 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.071 0.035 199.7 74: (ns/day) (hour/ns) 74: Performance: 41.554 0.578 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (87 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.083 0.041 199.6 74: (ns/day) (hour/ns) 74: Performance: 35.450 0.677 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.063 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 46.369 0.518 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (108 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (3716 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 46 tests from 3 test suites ran. (6429 ms total) 74: [ PASSED ] 46 tests. 74/94 Test #74: MdrunNonIntegratorTests ...................... Passed 6.72 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (169 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (155 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (156 ms) 75: [----------] 3 tests from Simple/TpiTest (481 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (486 ms total) 75: [ PASSED ] 3 tests. 75/94 Test #75: MdrunTpiTests ................................ Passed 0.56 sec test 76 Start 76: MdrunMpiTests 76: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Setting the LD random seed to -1480591114 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: This run will generate roughly 0 Mb of data 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 21 % of the run time was spent in domain decomposition, 76: 41 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.240 0.060 399.8 76: (ns/day) (hour/ns) 76: Performance: 1.440 16.671 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: [ OK ] MimicTest.OneQuantumMol (124 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: Setting the LD random seed to 536474558 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 54 % of the run time was spent in domain decomposition, 76: 17 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.004 0.251 400.0 76: (ns/day) (hour/ns) 76: Performance: 0.344 69.733 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: [ OK ] MimicTest.AllQuantumMol (299 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: Setting the LD random seed to -55599941 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 52 % of the run time was spent in domain decomposition, 76: 33 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.057 0.014 399.2 76: (ns/day) (hour/ns) 76: Performance: 6.065 3.957 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (34 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Setting the LD random seed to 2102329339 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 47 % of the run time was spent in domain decomposition, 76: 34 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.060 0.015 399.0 76: (ns/day) (hour/ns) 76: Performance: 5.739 4.182 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (33 ms) 76: [----------] 4 tests from MimicTest (491 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Setting the LD random seed to -35851019 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -393217 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 2068447039 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -76546433 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 9.4%. 76: The balanceable part of the MD step is 54%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 5.0%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: NOTE: 5.0 % of the available CPU time was lost due to load imbalance 76: in the domain decomposition. 76: You can consider manually changing the decomposition (option -dd); 76: e.g. by using fewer domains along the box dimension in which there is 76: considerable inhomogeneity in the simulated system. 76: 76: NOTE: 19 % of the run time was spent in domain decomposition, 76: 9 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.478 0.120 398.5 76: (ns/day) (hour/ns) 76: Performance: 15.122 1.587 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (132 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.450 0.113 399.8 76: (ns/day) (hour/ns) 76: Performance: 16.121 1.489 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (128 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 7.1%. 76: The balanceable part of the MD step is 22%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.6%. 76: 76: 76: NOTE: 14 % of the run time was spent in domain decomposition, 76: 4 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.340 0.335 399.8 76: (ns/day) (hour/ns) 76: Performance: 5.414 4.433 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (10429 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.735 0.184 399.7 76: (ns/day) (hour/ns) 76: Performance: 9.864 2.433 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (5808 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.892 0.223 399.6 76: (ns/day) (hour/ns) 76: Performance: 8.133 2.951 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (255 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.510 0.128 399.5 76: (ns/day) (hour/ns) 76: Performance: 14.224 1.687 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (153 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (16909 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (17433 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/94 Test #76: MdrunMpiTests ................................ Passed 17.62 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 6 tests from 2 test suites. 77: [----------] Global test environment set-up. 77: [----------] 4 tests from InNvt/MultiSimTest 77: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Setting the LD random seed to 1576924735 77: Setting the LD random seed to -92275781 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -3212293 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -1379996151 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -137625985 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -627053089 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -87199753 77: 77: Velocities were taken from a Maxwell distribution at 268 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -2173249 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (70 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 77: Setting the LD random seed to -605088265 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -1277232661 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: Setting the LD random seed to -14738818 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -639250481 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 33 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 33 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (27 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 77: Setting the LD random seed to -31724579 77: Setting the LD random seed to -126091281 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: 77: Setting gen_seed to -9176644 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -20008457 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -315752523 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -132361 77: 77: Velocities were taken from a Maxwell distribution at 268 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -1091698719 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -545330225 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 3 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 0 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: NOTE: 17 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (51 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 77: Setting the LD random seed to 2129621623 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -1510474180 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -1073742088 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -33596577 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 0 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: NOTE: 23 % of the run time was spent in domain decomposition, 77: 13 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: NOTE: 30 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (53 ms) 77: [----------] 4 tests from InNvt/MultiSimTest (223 ms total) 77: 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: Setting the LD random seed to 1878719151 77: Setting the LD random seed to 2013187036 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Setting gen_seed to -30541669 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Setting gen_seed to -3146818 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -476059794 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to 1610512862 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -1090560007 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to 1999486351 77: 77: Velocities were taken from a Maxwell distribution at 268 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Step 13: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: NOTE: 14 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps (continuing from step 14, 0.0 ps). 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: 77: Step 11: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: NOTE: 15 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 14 steps, 0.0 ps (continuing from step 12, 0.0 ps). 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: 77: Step 14: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: NOTE: 13 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 17 steps, 0.0 ps (continuing from step 15, 0.0 ps). 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: 77: Step 4: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 7 steps, 0.0 ps (continuing from step 5, 0.0 ps). 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (30 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: Setting the LD random seed to 1744656191 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -145175042 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: Using 1 OpenMP thread per MPI process 77: 77: Setting the LD random seed to 2145377246 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -33965220 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.2%. 77: The balanceable part of the MD step is 7%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.2%. 77: 77: 77: NOTE: 27 % of the run time was spent in domain decomposition, 77: 8 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 22 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 77: 77: Writing final coordinates. 77: 77: NOTE: 37 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 7.1%. 77: The balanceable part of the MD step is 7%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.5%. 77: 77: 77: NOTE: 25 % of the run time was spent in domain decomposition, 77: 8 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 24 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 77: 77: Writing final coordinates. 77: 77: NOTE: 37 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (31 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (76 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 6 tests from 2 test suites ran. (363 ms total) 77: [ PASSED ] 6 tests. 77/94 Test #77: MdrunMultiSimTests ........................... Passed 1.13 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 5 tests from 2 test suites. 78: [----------] Global test environment set-up. 78: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Setting the LD random seed to 1432336895 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 2147074039 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Setting the LD random seed to -134415105 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 419430396 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -71634754 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1914864642 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Setting the LD random seed to -1093018113 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 2143148031 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (38 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 78: Setting the LD random seed to -562561145 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -2025981921 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Setting the LD random seed to 2112830839 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 1995702203 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1615881605 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -587436073 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -19473473 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1229205833 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (19 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 78: Setting the LD random seed to -318771329 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -671481891 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to 1072627455 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -414196051 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.6%. 78: The balanceable part of the MD step is 11%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.1%. 78: 78: 78: NOTE: 13 % of the run time was spent in domain decomposition, 78: 4 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.6%. 78: The balanceable part of the MD step is 11%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.1%. 78: 78: 78: NOTE: 12 % of the run time was spent in domain decomposition, 78: 4 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 32 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (19 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 78: Setting the LD random seed to -436217417 78: Setting the LD random seed to -100684803 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -232589313 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 1308094207 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.3%. 78: The balanceable part of the MD step is 11%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.0%. 78: 78: 78: NOTE: 14 % of the run time was spent in domain decomposition, 78: 4 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 29 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.1%. 78: The balanceable part of the MD step is 12%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.0%. 78: 78: 78: NOTE: 14 % of the run time was spent in domain decomposition, 78: 4 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 29 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (38 ms) 78: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (122 ms total) 78: 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Setting the LD random seed to -1110454833 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -134234195 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to 1340072657 78: 78: Setting the LD random seed to 2109569010 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -83888129 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -126952773 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -70842913 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -880828421 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 78: 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: Writing final coordinates. 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 78: 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: 78: Writing final coordinates. 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: 78: Writing final coordinates. 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (52 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (52 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 5 tests from 2 test suites ran. (260 ms total) 78: [ PASSED ] 5 tests. 78/94 Test #78: MdrunMultiSimReplexTests ..................... Passed 0.76 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 10 tests from 2 test suites. 79: [----------] Global test environment set-up. 79: [----------] 8 tests from LF/ReplicaExchangeTest 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (381 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (470 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 3 NOTEs 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 3 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (364 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (361 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.1%. 79: The balanceable part of the MD step is 45%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.0%. 79: The balanceable part of the MD step is 45%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: 79: NOTE: 14 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (394 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 0.3%. 79: The balanceable part of the MD step is 47%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.2%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.6%. 79: The balanceable part of the MD step is 47%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.8%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (329 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 3 NOTEs 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 0.9%. 79: The balanceable part of the MD step is 46%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.5%. 79: The balanceable part of the MD step is 47%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.7%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (394 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 0.5%. 79: The balanceable part of the MD step is 47%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.2%. 79: 79: 79: NOTE: 14 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 2.0%. 79: The balanceable part of the MD step is 47%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 1.0%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (347 ms) 79: [----------] 8 tests from LF/ReplicaExchangeTest (3108 ms total) 79: 79: [----------] 2 tests from VV/ReplicaExchangeTest 79: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (458 ms) 79: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.1%. 79: The balanceable part of the MD step is 37%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: 79: NOTE: 12 % of the run time was spent in domain decomposition, 79: 4 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 7 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 0.5%. 79: The balanceable part of the MD step is 36%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.2%. 79: 79: 79: NOTE: 13 % of the run time was spent in domain decomposition, 79: 3 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 8 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (273 ms) 79: [----------] 2 tests from VV/ReplicaExchangeTest (752 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 10 tests from 2 test suites ran. (3928 ms total) 79: [ PASSED ] 10 tests. 79/94 Test #79: MdrunMultiSimReplexEquivalenceTests .......... Passed 4.30 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Setting the LD random seed to -340365674 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to 2107367141 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.1 80: (ns/day) (hour/ns) 80: Performance: 131.110 0.183 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (10464 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.2 80: (ns/day) (hour/ns) 80: Performance: 130.208 0.184 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (19 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.0 80: (ns/day) (hour/ns) 80: Performance: 66.579 0.360 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (32811 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 198.8 80: (ns/day) (hour/ns) 80: Performance: 179.990 0.133 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (23 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (43321 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (43335 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/94 Test #80: MdrunMpi1RankPmeTests ........................ Passed 43.65 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Setting the LD random seed to -437481061 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Setting the LD random seed to -393270 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.9%. 81: The balanceable part of the MD step is 1%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.0%. 81: 81: 81: NOTE: 20 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.351 0.088 399.6 81: (ns/day) (hour/ns) 81: Performance: 20.631 1.163 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (11275 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 24.8%. 81: The balanceable part of the MD step is 20%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.9%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: Core t (s) Wall t (s) (%) 81: Time: 2.258 0.565 400.0 81: (ns/day) (hour/ns) 81: Performance: 3.214 7.468 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (664 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 44 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.432 0.109 397.7 81: (ns/day) (hour/ns) 81: Performance: 0.795 30.173 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (34683 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.858 0.215 399.7 81: (ns/day) (hour/ns) 81: Performance: 8.455 2.838 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (5979 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.824 0.208 395.6 81: (ns/day) (hour/ns) 81: Performance: 8.711 2.755 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (229 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.237 0.060 397.6 81: (ns/day) (hour/ns) 81: Performance: 1.448 16.570 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (21541 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 30.3%. 81: The balanceable part of the MD step is 25%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.6%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.864 0.216 399.9 81: (ns/day) (hour/ns) 81: Performance: 8.395 2.859 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (276 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (74656 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (74695 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/94 Test #81: MdrunMpi2RankPmeTests ........................ Passed 75.12 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 97.8 82: (ns/day) (hour/ns) 82: Performance: 949.683 0.025 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2435.980 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2383.208 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.2 82: (ns/day) (hour/ns) 82: Performance: 2452.466 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 94.5 82: (ns/day) (hour/ns) 82: Performance: 2431.174 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.1 82: (ns/day) (hour/ns) 82: Performance: 2519.670 0.010 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (37 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (37 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (41 ms total) 82: [ PASSED ] 1 test. 82/94 Test #82: MdrunCoordinationBasicTests1Rank ............. Passed 0.37 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 7%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 53 % of the run time was spent in domain decomposition, 83: 1 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 18 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.008 0.004 197.4 83: (ns/day) (hour/ns) 83: Performance: 365.484 0.066 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 29 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1626.345 0.015 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.5%. 83: The balanceable part of the MD step is 46%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 87 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.009 0.005 197.4 83: (ns/day) (hour/ns) 83: Performance: 310.796 0.077 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.4 83: (ns/day) (hour/ns) 83: Performance: 1698.069 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 35 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1715.565 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.8%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 189.3 83: (ns/day) (hour/ns) 83: Performance: 1736.846 0.014 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (211 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (211 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (257 ms total) 83: [ PASSED ] 1 test. 83/94 Test #83: MdrunCoordinationBasicTests2Ranks ............ Passed 0.48 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.002 97.9 84: (ns/day) (hour/ns) 84: Performance: 912.545 0.026 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2193.944 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2757.652 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2548.860 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2532.098 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2345.999 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (41 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1942.180 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2349.578 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2587.398 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2274.121 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2384.131 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.5 84: (ns/day) (hour/ns) 84: Performance: 2429.256 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1869.679 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2142.815 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2341.541 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2396.186 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2410.248 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2425.431 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (37 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1911.447 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2259.110 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2577.654 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2248.392 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2454.420 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 91.8 84: (ns/day) (hour/ns) 84: Performance: 2231.291 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2033.870 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2392.464 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.5 84: (ns/day) (hour/ns) 84: Performance: 2730.760 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2370.371 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2547.806 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2556.263 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1820.506 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2354.967 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2536.267 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2466.210 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2466.210 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2515.555 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2002.794 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2274.121 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1377.901 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2352.269 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2489.129 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 91.6 84: (ns/day) (hour/ns) 84: Performance: 2263.260 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1966.356 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2373.110 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2698.464 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2494.167 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 1565.589 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2391.535 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2102.592 0.011 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2452.466 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2190.823 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2498.213 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 92.1 84: (ns/day) (hour/ns) 84: Performance: 2375.856 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2523.799 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1630.218 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2289.332 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2717.509 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2383.208 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2473.141 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 1785.162 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1921.583 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2325.630 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2696.102 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 1950.172 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2456.377 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2454.420 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2046.029 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2371.283 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 14 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.6 84: (ns/day) (hour/ns) 84: Performance: 2151.797 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2459.319 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2422.569 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2454.420 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1829.155 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2345.106 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2651.999 0.009 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2208.890 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2419.715 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2445.651 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1901.418 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2239.402 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2349.578 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2322.999 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2291.888 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2274.121 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1812.472 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2103.310 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2506.344 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2333.558 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2303.026 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2265.757 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1892.074 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2139.838 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2259.110 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2276.642 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2249.213 0.011 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2340.651 0.010 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1562.413 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1848.918 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1993.075 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1857.279 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1866.847 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1785.679 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1477.006 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1655.629 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1731.477 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1587.782 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1737.336 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1673.620 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1463.324 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1614.411 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1726.140 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1736.357 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 1668.633 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1753.656 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1563.206 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1593.120 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 1942.792 0.012 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 1777.436 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 1716.043 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 1719.395 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1466.459 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1625.058 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1806.096 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 1544.783 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 1704.647 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1703.233 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (33 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1320.033 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1753.656 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1866.847 0.013 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 87.7 84: (ns/day) (hour/ns) 84: Performance: 1489.505 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1710.326 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1721.317 0.014 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1346.284 0.018 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1088.252 0.022 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1579.234 0.015 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1492.392 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 10 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1289.367 0.019 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1452.970 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.002 96.7 84: (ns/day) (hour/ns) 84: Performance: 937.258 0.026 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1114.434 0.022 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1090.950 0.022 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1127.282 0.021 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1128.107 0.021 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1136.012 0.021 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1270.487 0.019 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1178.610 0.020 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (35 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1480.200 0.016 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1193.220 0.020 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1404.604 0.017 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1349.232 0.018 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (33 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (805 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (809 ms total) 84: [ PASSED ] 25 tests. 84/94 Test #84: MdrunCoordinationCouplingTests1Rank .......... Passed 1.06 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 194.6 85: (ns/day) (hour/ns) 85: Performance: 737.840 0.033 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 19 % of the run time was spent in domain decomposition, 85: 4 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1359.804 0.018 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/TestinOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 g/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 2019.867 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1813.273 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.0%. 85: The balanceable part of the MD step is 3%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 86 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 198.2 85: (ns/day) (hour/ns) 85: Performance: 279.938 0.086 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.9%. 85: The balanceable part of the MD step is 35%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1833.510 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (51 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1405.405 0.017 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 74.4%. 85: The balanceable part of the MD step is 19%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 14.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 14.3 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 18 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.6 85: (ns/day) (hour/ns) 85: Performance: 208.191 0.115 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly cOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 orrect ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.5 85: (ns/day) (hour/ns) 85: Performance: 1764.455 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1753.906 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 167.1 85: (ns/day) (hour/ns) 85: Performance: 1196.348 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1675.212 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (39 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.5 85: (ns/day) (hour/ns) 85: Performance: 1363.717 0.018 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1587.168 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 odicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriGenerated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1758.662 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 87 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 191.2 85: (ns/day) (hour/ns) 85: Performance: 287.851 0.083 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1707.955 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1720.116 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (48 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.7%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.4%. 85: 85: 85: NOTE: 83 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.0 85: (ns/day) (hour/ns) 85: Performance: 301.753 0.080 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1558.263 0.015 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1754.155 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1668.181 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.5 85: (ns/day) (hour/ns) 85: Performance: 1721.558 0.014 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1739.298 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (40 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 198.2 85: (ns/day) (hour/ns) 85: Performance: 281.460 0.085 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1853.646 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.6 85: (ns/day) (hour/ns) 85: Performance: 2070.788 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 2018.543 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1991.786 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 1899.659 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1513.659 0.016 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (45 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1710.326 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.5 85: (ns/day) (hour/ns) 85: Performance: 294.294 0.082 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.4 85: (ns/day) (hour/ns) 85: Performance: 1838.434 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1882.534 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 86 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.9 85: (ns/day) (hour/ns) 85: Performance: 287.060 0.084 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1459.338 0.016 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (53 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1671.349 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1876.513 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1823.740 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1787.493 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.3 85: (ns/day) (hour/ns) 85: Performance: 1874.515 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (41 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1432.863 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.5 85: (ns/day) (hour/ns) 85: Performance: 1747.438 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.8 85: (ns/day) (hour/ns) 85: Performance: 1867.696 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1762.184 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 1828.069 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1695.498 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (45 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1569.378 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1746.200 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 87 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.009 0.005 196.6 85: (ns/day) (hour/ns) 85: Performance: 308.771 0.078 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.2 85: (ns/day) (hour/ns) 85: Performance: 1946.783 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.5 85: (ns/day) (hour/ns) 85: Performance: 1962.285 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.7 85: (ns/day) (hour/ns) 85: Performance: 1950.481 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (41 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 85 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.1 85: (ns/day) (hour/ns) 85: Performance: 291.591 0.082 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1732.450 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly corrOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 ect ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.1 85: (ns/day) (hour/ns) 85: Performance: 1939.428 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 88 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.9 85: (ns/day) (hour/ns) 85: Performance: 285.140 0.084 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.2 85: (ns/day) (hour/ns) 85: Performance: 1855.042 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.0 85: (ns/day) (hour/ns) 85: Performance: 1857.839 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (47 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 198.0 85: (ns/day) (hour/ns) 85: Performance: 277.974 0.086 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1770.540 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 2007.035 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1869.679 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.4 85: (ns/day) (hour/ns) 85: Performance: 1891.784 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1910.854 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (55 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1428.212 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1744.469 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.1 85: (ns/day) (hour/ns) 85: Performance: 1852.532 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.5 85: (ns/day) (hour/ns) 85: Performance: 1867.696 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 88 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.009 0.005 196.3 85: (ns/day) (hour/ns) 85: Performance: 315.580 0.076 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.5 85: (ns/day) (hour/ns) 85: Performance: 1855.042 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.1 85: (ns/day) (hour/ns) 85: Performance: 1527.736 0.016 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (46 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1741.511 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1938.208 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 2032.864 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 2017.882 0.012 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 84 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 198.0 85: (ns/day) (hour/ns) 85: Performance: 291.240 0.082 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1509.210 0.016 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (43 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1711.989 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1918.590 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1821.852 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1748.430 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 87 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.009 0.005 194.5 85: (ns/day) (hour/ns) 85: Performance: 311.566 0.077 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.7 85: (ns/day) (hour/ns) 85: Performance: 1507.363 0.016 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (47 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1663.452 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1855.601 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1750.666 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1786.197 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1764.202 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (58 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1391.438 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1665.701 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1684.603 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.6 85: (ns/day) (hour/ns) 85: Performance: 1774.876 0.014 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1823.470 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1789.570 0.013 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (58 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 8%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 196.6 85: (ns/day) (hour/ns) 85: Performance: 256.964 0.093 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 59%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.7 85: (ns/day) (hour/ns) 85: Performance: 1106.727 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.5 85: (ns/day) (hour/ns) 85: Performance: 1238.684 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 9.6%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 14 % of the run time was spent in domain decomposition, 85: 3 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 21 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.6 85: (ns/day) (hour/ns) 85: Performance: 957.878 0.025 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.2 85: (ns/day) (hour/ns) 85: Performance: 1205.714 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 5.6%. 85: The balanceable part of the MD step is 29%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.6%. 85: 85: 85: NOTE: 21 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 188.0 85: (ns/day) (hour/ns) 85: Performance: 936.688 0.026 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (46 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.8 85: (ns/day) (hour/ns) 85: Performance: 945.601 0.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 42 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 196.7 85: (ns/day) (hour/ns) 85: Performance: 251.679 0.095 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.3 85: (ns/day) (hour/ns) 85: Performance: 1094.050 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.9 85: (ns/day) (hour/ns) 85: Performance: 1092.304 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.6 85: (ns/day) (hour/ns) 85: Performance: 1090.467 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.4%. 85: The balanceable part of the MD step is 5%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.0%. 85: 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 196.4 85: (ns/day) (hour/ns) 85: Performance: 263.589 0.091 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (52 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 23 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.2 85: (ns/day) (hour/ns) 85: Performance: 932.929 0.026 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.9 85: (ns/day) (hour/ns) 85: Performance: 1047.364 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 82 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 195.9 85: (ns/day) (hour/ns) 85: Performance: 260.909 0.092 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.2 85: (ns/day) (hour/ns) 85: Performance: 1044.257 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 6%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 80 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 196.1 85: (ns/day) (hour/ns) 85: Performance: 251.345 0.095 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 5.2%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 187.0 85: (ns/day) (hour/ns) 85: Performance: 997.021 0.024 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (51 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.4 85: (ns/day) (hour/ns) 85: Performance: 1055.167 0.023 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.005 196.0 85: (ns/day) (hour/ns) 85: Performance: 267.683 0.090 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.6 85: (ns/day) (hour/ns) 85: Performance: 1287.211 0.019 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 182.7 85: (ns/day) (hour/ns) 85: Performance: 1197.511 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.1 85: (ns/day) (hour/ns) 85: Performance: 1154.859 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.1 85: (ns/day) (hour/ns) 85: Performance: 1183.137 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (49 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.2 85: (ns/day) (hour/ns) 85: Performance: 988.939 0.024 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 184.0 85: (ns/day) (hour/ns) 85: Performance: 1043.373 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_inpuOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 t.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.8 85: (ns/day) (hour/ns) 85: Performance: 1175.574 0.020 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 195.8 85: (ns/day) (hour/ns) 85: Performance: 257.992 0.093 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.4 85: (ns/day) (hour/ns) 85: Performance: 1135.489 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.4 85: (ns/day) (hour/ns) 85: Performance: 1115.241 0.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (51 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.2 85: (ns/day) (hour/ns) 85: Performance: 1009.685 0.024 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 184.4 85: (ns/day) (hour/ns) 85: Performance: 1038.448 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.6 85: (ns/day) (hour/ns) 85: Performance: 1138.531 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 184.5 85: (ns/day) (hour/ns) 85: Performance: 1062.446 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.1 85: (ns/day) (hour/ns) 85: Performance: 1141.696 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.2 85: (ns/day) (hour/ns) 85: Performance: 1123.171 0.021 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (42 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.5 85: (ns/day) (hour/ns) 85: Performance: 884.000 0.027 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.2 85: (ns/day) (hour/ns) 85: Performance: 947.929 0.025 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 185.4 85: (ns/day) (hour/ns) 85: Performance: 948.148 0.025 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.8 85: (ns/day) (hour/ns) 85: Performance: 1002.130 0.024 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 196.1 85: (ns/day) (hour/ns) 85: Performance: 253.173 0.095 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.1 85: (ns/day) (hour/ns) 85: Performance: 1011.592 0.024 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (49 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 189.5 85: (ns/day) (hour/ns) 85: Performance: 637.017 0.038 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 187.2 85: (ns/day) (hour/ns) 85: Performance: 734.103 0.033 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settiOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 ngs require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.9 85: (ns/day) (hour/ns) 85: Performance: 869.036 0.028 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.007 0.004 193.0 85: (ns/day) (hour/ns) 85: Performance: 393.787 0.061 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.0 85: (ns/day) (hour/ns) 85: Performance: 788.606 0.030 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.7 85: (ns/day) (hour/ns) 85: Performance: 785.890 0.031 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (45 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.6 85: (ns/day) (hour/ns) 85: Performance: 882.796 0.027 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.9 85: (ns/day) (hour/ns) 85: Performance: 860.358 0.028 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.5 85: (ns/day) (hour/ns) 85: Performance: 1062.171 0.023 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.1 85: (ns/day) (hour/ns) 85: Performance: 897.326 0.027 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (45 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1207 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (1214 ms total) 85: [ PASSED ] 25 tests. 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 172.7 85: (ns/day) (hour/ns) 85: Performance: 913.019 0.026 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 185.6 85: (ns/day) (hour/ns) 85: Performance: 993.885 0.024 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85/94 Test #85: MdrunCoordinationCouplingTests2Ranks ......... Passed 1.70 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1663.227 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 1947.706 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2363.097 0.010 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.4 86: (ns/day) (hour/ns) 86: Performance: 2145.801 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2139.095 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2118.499 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (959 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1372.070 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 1948.938 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 1790.350 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 1741.757 0.014 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.0 86: (ns/day) (hour/ns) 86: Performance: 2100.441 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1419.165 0.017 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (952 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1673.165 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 1968.241 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2273.282 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 16 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 1819.431 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2142.815 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2191.602 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (944 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1683.682 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1949.555 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2288.482 0.010 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2230.483 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 14 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 1862.332 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2258.282 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (954 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1413.629 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 1930.011 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.2 86: (ns/day) (hour/ns) 86: Performance: 2234.528 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.4 86: (ns/day) (hour/ns) 86: Performance: 2126.543 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2183.833 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2245.933 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (970 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1755.155 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 2041.960 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2319.501 0.010 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2169.987 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.2 86: (ns/day) (hour/ns) 86: Performance: 2083.393 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2221.635 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (944 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1692.936 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1904.357 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2160.096 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2004.749 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2095.440 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2115.589 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (947 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1359.054 0.018 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1925.186 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2154.807 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2078.473 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 1932.432 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1874.800 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (967 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1605.994 0.015 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1817.284 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 2096.153 0.011 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 1955.123 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1987.288 0.012 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 1796.615 0.013 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (999 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.7 86: (ns/day) (hour/ns) 86: Performance: 1022.335 0.023 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.1 86: (ns/day) (hour/ns) 86: Performance: 1479.845 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 31 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.6 86: (ns/day) (hour/ns) 86: Performance: 1063.638 0.023 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1324.005 0.018 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.8 86: (ns/day) (hour/ns) 86: Performance: 1314.120 0.018 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1482.337 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (981 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 97.8 86: (ns/day) (hour/ns) 86: Performance: 880.714 0.027 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1245.319 0.019 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.9 86: (ns/day) (hour/ns) 86: Performance: 1461.935 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.9 86: (ns/day) (hour/ns) 86: Performance: 1352.490 0.018 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.003 0.003 98.5 86: (ns/day) (hour/ns) 86: Performance: 432.565 0.055 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1405.566 0.017 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (977 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1254.448 0.019 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1445.809 0.017 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1451.259 0.017 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1479.845 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.2 86: (ns/day) (hour/ns) 86: Performance: 275.395 0.087 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1047.898 0.023 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (989 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 10 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.8 86: (ns/day) (hour/ns) 86: Performance: 997.183 0.024 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.3 86: (ns/day) (hour/ns) 86: Performance: 1207.723 0.020 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1472.065 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1273.113 0.019 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1423.756 0.017 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1459.165 0.016 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (989 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (12581 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (12585 ms total) 86: [ PASSED ] 13 tests. 86/94 Test #86: MdrunCoordinationConstraintsTests1Rank ....... Passed 12.98 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.9%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.3 87: (ns/day) (hour/ns) 87: Performance: 1305.487 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 5%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.0%. 87: 87: 87: NOTE: 84 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.011 0.005 198.1 87: (ns/day) (hour/ns) 87: Performance: 272.810 0.088 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.9%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1704.175 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1701.821 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.8%. 87: The balanceable part of the MD step is 37%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 1724.690 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1686.910 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1059 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1269.048 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.3 87: (ns/day) (hour/ns) 87: Performance: 1505.337 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1720.116 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 26%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 26 % of the run time was spent in domain decomposition, 87: 4 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.8 87: (ns/day) (hour/ns) 87: Performance: 1228.678 0.020 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 179.6 87: (ns/day) (hour/ns) 87: Performance: 1391.438 0.017 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1518.135 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (998 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 15 % of the run time was spent in domain decomposition, 87: 4 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 191.7 87: (ns/day) (hour/ns) 87: Performance: 1115.443 0.022 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1466.983 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1618.228 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1627.419 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 194.5 87: (ns/day) (hour/ns) 87: Performance: 663.571 0.036 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1485.913 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1015 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1289.367 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1661.209 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1667.278 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.2 87: (ns/day) (hour/ns) 87: Performance: 1673.392 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1705.591 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1759.164 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1044 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1327.857 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1512.916 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1686.679 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.1 87: (ns/day) (hour/ns) 87: Performance: 1616.954 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.4 87: (ns/day) (hour/ns) 87: Performance: 1677.493 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.0 87: (ns/day) (hour/ns) 87: Performance: 1645.458 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1088 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.0 87: (ns/day) (hour/ns) 87: Performance: 1344.961 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1598.079 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1750.666 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.5 87: (ns/day) (hour/ns) 87: Performance: 1716.521 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1687.603 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1419.655 0.017 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1054 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.3 87: (ns/day) (hour/ns) 87: Performance: 1330.582 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1519.821 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1740.772 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1731.477 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1730.747 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1696.900 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1018 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.3 87: (ns/day) (hour/ns) 87: Performance: 1304.658 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1490.947 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.3 87: (ns/day) (hour/ns) 87: Performance: 1683.452 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1343.494 0.018 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1601.402 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1671.803 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (944 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.9 87: (ns/day) (hour/ns) 87: Performance: 1300.252 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1481.268 0.016 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1687.141 0.014 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1575.599 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1565.788 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1565.390 0.015 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1050 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 60%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 188.4 87: (ns/day) (hour/ns) 87: Performance: 931.941 0.026 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 59%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 187.3 87: (ns/day) (hour/ns) 87: Performance: 1019.459 0.024 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 4.3%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.0%. 87: 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.5 87: (ns/day) (hour/ns) 87: Performance: 1161.281 0.021 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 44%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 173.5 87: (ns/day) (hour/ns) 87: Performance: 1029.339 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.8%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 185.6 87: (ns/day) (hour/ns) 87: Performance: 1118.989 0.021 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 185.7 87: (ns/day) (hour/ns) 87: Performance: 1095.217 0.022 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1027 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.8 87: (ns/day) (hour/ns) 87: Performance: 880.273 0.027 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.5 87: (ns/day) (hour/ns) 87: Performance: 963.195 0.025 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 187.2 87: (ns/day) (hour/ns) 87: Performance: 1056.253 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.8 87: (ns/day) (hour/ns) 87: Performance: 1010.513 0.024 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.9 87: (ns/day) (hour/ns) 87: Performance: 859.938 0.028 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.3 87: (ns/day) (hour/ns) 87: Performance: 1044.877 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1025 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 184.4 87: (ns/day) (hour/ns) 87: Performance: 886.863 0.027 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.9 87: (ns/day) (hour/ns) 87: Performance: 1009.437 0.024 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 183.8 87: (ns/day) (hour/ns) 87: Performance: 1023.780 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 183.2 87: (ns/day) (hour/ns) 87: Performance: 1065.570 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 183.9 87: (ns/day) (hour/ns) 87: Performance: 1103.752 0.022 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 183.5 87: (ns/day) (hour/ns) 87: Performance: 1116.555 0.021 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1011 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 185.9 87: (ns/day) (hour/ns) 87: Performance: 930.322 0.026 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.8 87: (ns/day) (hour/ns) 87: Performance: 1020.219 0.024 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 184.9 87: (ns/day) (hour/ns) 87: Performance: 959.519 0.025 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 177.3 87: (ns/day) (hour/ns) 87: Performance: 952.326 0.025 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 184.3 87: (ns/day) (hour/ns) 87: Performance: 1041.256 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 183.9 87: (ns/day) (hour/ns) 87: Performance: 1053.453 0.023 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1051 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (13396 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (13407 ms total) 87: [ PASSED ] 13 tests. 87/94 Test #87: MdrunCoordinationConstraintsTests2Ranks ...... Passed 13.67 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.032 0.016 199.4 88: (ns/day) (hour/ns) 88: Performance: 91.329 0.263 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.024 0.012 198.4 88: (ns/day) (hour/ns) 88: Performance: 64.136 0.374 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (69 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.013 0.006 198.7 88: (ns/day) (hour/ns) 88: Performance: 26.968 0.890 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (29 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (99 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1245612551 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.066 0.033 199.6 88: (ns/day) (hour/ns) 88: Performance: 55.188 0.435 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10481 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -138412075 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.080 0.040 199.6 88: (ns/day) (hour/ns) 88: Performance: 44.998 0.533 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (127 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1084343810 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.072 0.036 199.6 88: (ns/day) (hour/ns) 88: Performance: 50.165 0.478 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (123 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -4203781 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.053 0.027 199.5 88: (ns/day) (hour/ns) 88: Performance: 67.868 0.354 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (12799 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -1075454737 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.060 0.030 199.6 88: (ns/day) (hour/ns) 88: Performance: 60.815 0.395 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (44 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to -537952769 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.329 0.165 199.9 88: (ns/day) (hour/ns) 88: Performance: 52.982 0.453 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (260 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1928705403 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.138 0.069 199.8 88: (ns/day) (hour/ns) 88: Performance: 26.298 0.913 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (147 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -16916781 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.090 0.045 199.8 88: (ns/day) (hour/ns) 88: Performance: 40.116 0.598 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (128 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -671561479 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.041 0.021 199.3 88: (ns/day) (hour/ns) 88: Performance: 88.078 0.272 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (99 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.034 0.017 199.3 88: (ns/day) (hour/ns) 88: Performance: 107.922 0.222 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -1216398299 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.90 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (108 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -683695329 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.068 0.034 199.7 88: (ns/day) (hour/ns) 88: Performance: 53.176 0.451 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (119 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1123289601 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.90 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.025 0.013 199.1 88: (ns/day) (hour/ns) 88: Performance: 141.837 0.169 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (88 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (24529 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (24644 ms total) 88: [ PASSED ] 14 tests. 88/94 Test #88: MdrunFEPTests ................................ Passed 24.73 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 18 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.888 0.444 200.0 89: (ns/day) (hour/ns) 89: Performance: 4.085 5.876 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (687 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.080 0.040 199.6 89: (ns/day) (hour/ns) 89: Performance: 45.338 0.529 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (223 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 13 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.504 0.752 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.412 9.948 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (928 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.088 0.044 199.6 89: (ns/day) (hour/ns) 89: Performance: 41.339 0.581 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (207 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (2047 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (2052 ms total) 89: [ PASSED ] 4 tests. 89/94 Test #89: MdrunPullTests ............................... Passed 2.37 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -419693058 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.024 0.012 199.0 90: (ns/day) (hour/ns) 90: Performance: 368.734 0.065 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (35 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -809664561 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.008 0.004 196.7 90: (ns/day) (hour/ns) 90: Performance: 1109.590 0.022 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (19 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1115690562 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.055 0.028 199.5 90: (ns/day) (hour/ns) 90: Performance: 162.440 0.148 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (35 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1073873425 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.013 199.0 90: (ns/day) (hour/ns) 90: Performance: 356.249 0.067 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (63 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1881342982 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.179 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 50.170 0.478 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (97 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1677301738 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.179 0.089 199.9 90: (ns/day) (hour/ns) 90: Performance: 50.220 0.478 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (97 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1018003391 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.060 0.030 199.5 90: (ns/day) (hour/ns) 90: Performance: 150.515 0.159 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (37 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -142644785 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.002 0.001 192.6 90: (ns/day) (hour/ns) 90: Performance: 5268.149 0.005 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (11 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1177289025 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.003 0.002 195.7 90: (ns/day) (hour/ns) 90: Performance: 2569.076 0.009 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (11 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -255983809 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.007 0.004 196.2 90: (ns/day) (hour/ns) 90: Performance: 1262.253 0.019 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (8 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -572000403 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.013 0.006 197.8 90: (ns/day) (hour/ns) 90: Performance: 692.520 0.035 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (16 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -277219337 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.012 0.006 197.8 90: (ns/day) (hour/ns) 90: Performance: 716.045 0.034 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (15 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (450 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (455 ms total) 90: [ PASSED ] 12 tests. 90/94 Test #90: MdrunRotationTests ........................... Passed 0.54 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 0 tests from 0 test suites. 91: [==========] 0 tests from 0 test suites ran. (0 ms total) 91: [ PASSED ] 0 tests. 91: 91: YOU HAVE 82 DISABLED TESTS 91: 91/94 Test #91: MdrunSimulatorComparison ..................... Passed 0.10 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: This run will generate roughly 0 Mb of data 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 10.0%. 92: The balanceable part of the MD step is 36%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.7%. 92: 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.004 0.002 193.8 92: (ns/day) (hour/ns) 92: Performance: 414.421 0.058 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: trr version: GMX_trn_file (single precision) 92: Reading virtual site types... 92: 92: trr version: GMX_trn_file (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (11 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 9.7%. 92: The balanceable part of the MD step is 35%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.4%. 92: 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.2 92: (ns/day) (hour/ns) 92: Performance: 869.847 0.028 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (6 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: This run will generate roughly 0 Mb of data 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.6%. 92: The balanceable part of the MD step is 35%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.1%. 92: 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.0 92: (ns/day) (hour/ns) 92: Performance: 907.608 0.026 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (7 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 33 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 187.7 92: (ns/day) (hour/ns) 92: Performance: 907.104 0.026 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (18 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: This run will generate roughly 0 Mb of data 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 187.2 92: (ns/day) (hour/ns) 92: Performance: 972.708 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (15 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 32 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 186.4 92: (ns/day) (hour/ns) 92: Performance: 895.030 0.027 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (11 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 187.7 92: (ns/day) (hour/ns) 92: Performance: 997.550 0.024 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (12 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 186.7 92: (ns/day) (hour/ns) 92: Performance: 943.582 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (17 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 187.1 92: (ns/day) (hour/ns) 92: Performance: 954.909 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (11 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.5%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.8%. 92: 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.2 92: (ns/day) (hour/ns) 92: Performance: 877.571 0.027 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (6 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.5%. 92: The balanceable part of the MD step is 41%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.1%. 92: 92: 92: NOTE: 34 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.2 92: (ns/day) (hour/ns) 92: Performance: 712.505 0.034 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (6 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.1 92: (ns/day) (hour/ns) 92: Performance: 958.980 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (11 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 32 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 187.0 92: (ns/day) (hour/ns) 92: Performance: 898.606 0.027 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (14 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.7 92: (ns/day) (hour/ns) 92: Performance: 867.764 0.028 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (12 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.2 92: (ns/day) (hour/ns) 92: Performance: 874.277 0.027 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (13 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.8 92: (ns/day) (hour/ns) 92: Performance: 931.056 0.026 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (14 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 49 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 191.7 92: (ns/day) (hour/ns) 92: Performance: 626.126 0.038 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (10 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Reading virtual site types... 92: Reading virtual site types... 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.7 92: (ns/day) (hour/ns) 92: Performance: 963.370 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (14 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.9 92: (ns/day) (hour/ns) 92: Performance: 955.188 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (13 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 25 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 166.9 92: (ns/day) (hour/ns) 92: Performance: 707.022 0.034 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (14 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 31 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 187.6 92: (ns/day) (hour/ns) 92: Performance: 944.265 0.025 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (22 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (278 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (291 ms total) 92: [ PASSED ] 37 tests. 92/94 Test #92: MdrunVirtualSiteTests ........................ Passed 0.89 sec test 93 Start 93: EnsembleHistogramPotentialPlugin.ForceCalc 93: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" 93: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests 93: Test timeout computed to be: 1500 93: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 93: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc 93: [==========] Running 1 test from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 1 test from EnsembleHistogramPotentialPlugin 93: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc 93: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) 93: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 1 test from 1 test suite ran. (0 ms total) 93: [ PASSED ] 1 test. 93/94 Test #93: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.06 sec test 94 Start 94: EnsembleBoundingPotentialPlugin.ForceCalc 94: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" 94: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests 94: Test timeout computed to be: 1500 94: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 94: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from EnsembleBoundingPotentialPlugin 94: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc 94: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) 94: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (0 ms total) 94: [ PASSED ] 1 test. 94/94 Test #94: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.06 sec 100% tests passed, 0 tests failed out of 94 Label Time Summary: GTest = 1007.92 sec*proc (90 tests) IntegrationTest = 930.88 sec*proc (30 tests) MpiTest = 760.39 sec*proc (23 tests) QuickGpuTest = 109.38 sec*proc (22 tests) SlowGpuTest = 851.85 sec*proc (14 tests) SlowTest = 59.90 sec*proc (14 tests) UnitTest = 17.15 sec*proc (46 tests) Total Test time (real) = 383.43 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/documentation/lib cmake /build/reproducible-path/gromacs-2025.0 \ -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMXAPI=ON \ -DGMX_PYTHON_PACKAGE=ON -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON -DGMX_BUILD_HELP=ON \ -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2") -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.0/build/documentation/bin/gmx from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (35.3s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/documentation /usr/bin/make -j12 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 68 /usr/bin/make -f CMakeFiles/Makefile2 docs/manual/CMakeFiles/manual.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/sgangle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/sgangle.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/decomp.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/decomp.png /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/dih.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/dih.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/drift-all.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/drift-all.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-angle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/f-angle.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-bond.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/f-bond.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/adler32.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/compress.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/fp-highres.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/fp-highres.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/int-mat.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/int-mat.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/mdpar.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/mdpar.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/crc32.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/parsort.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/parsort.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/ring.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/ring.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/deflate.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/shiftf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/shiftf.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/dd-cells.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-cells.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/dd-tric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-tric.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/flowchart.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/flowchart.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/inffast.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free1.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free1.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inflate.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inflate.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inflate.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/inflate.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free2.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/leapfrog.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/leapfrog.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/lincs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/lincs.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/maxwell.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/maxwell.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/mpmd-pme.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/mpmd-pme.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/nstric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/nstric.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/par-lincs2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/par-lincs2.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/pbctric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/pbctric.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/inftrees.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/rhododec.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/rhododec.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/truncoct.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/truncoct.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/verlet-drift.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/verlet-drift.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/angle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/angle.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/bstretch.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/bstretch.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/chain.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/chain.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/trees.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/dummies.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/dummies.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-bham.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-bham.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fbposres.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/fbposres.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-dih.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-dih.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-dr.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-dr.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fig-02.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/fig-02.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fig-04.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/fig-04.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-imps.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-imps.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-lj.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-lj.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-morse.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-morse.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-pr.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-pr.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-rbs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-rbs.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/ring-imp.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/ring-imp.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/softcore.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/softcore.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/gapsys-sc.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/gapsys-sc.png [ 0%] Built target lmfit_objlib /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/muparser /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/subst-im.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/subst-im.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParser.cpp.o -MF CMakeFiles/muparser.dir/src/muParser.cpp.o.d -o CMakeFiles/muparser.dir/src/muParser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParser.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/tetra-im.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/tetra-im.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vcrf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/vcrf.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/uncompr.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vsite-4fdn.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/functions/plots/vsite-4fdn.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-invN.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/awh-invN.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-pmfs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/awh-pmfs.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/zutil.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-sampleweights.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/awh-sampleweights.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 1%] Built target tng_io_zlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_send_recv.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-traj.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/awh-traj.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/compelsetup.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/compelsetup.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/dumaro.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/dumaro.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/dumtypes.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/dumtypes.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/equipotential.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/equipotential.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/field.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/field.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/gaussians.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/gaussians.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/lambda-values.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/lambda-values.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pulldirrel.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/pulldirrel.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pull.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/pull.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pullref.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/pullref.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/rotation.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/special/plots/rotation.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/dih-def.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/dih-def.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserBase.cpp.o -MF CMakeFiles/muparser.dir/src/muParserBase.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserBase.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserBase.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/distm.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/distm.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hbond-insert.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/hbond-insert.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hbond.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/hbond.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hpr-wheel.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/hpr-wheel.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/msdwater.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/msdwater.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/phipsi.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/phipsi.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rama.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rama.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rdfO-O.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdfO-O.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rdf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdf.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-image-conversion-timestamp.txt cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c [ 7%] Built target sphinx-image-conversion /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.28 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2025.0/admin -D GMX_CLANG_MINIMUM_REQUIRED_VERSION=14 -D GMX_GCC_MINIMUM_REQUIRED_VERSION=11 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2025.0 -D GMX_CUDA_MINIMUM_REQUIRED_COMPUTE_CAPABILITY=5.0 -D GMX_CUDA_MINIMUM_REQUIRED_VERSION=12.1 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2025.0/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Brian Andrews, Vladimir Basov, Paul Bauer, Hugh Bird, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Petter Johansson, Carsten Kutzner, Grzegorz Łazarski, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Lukas Müllender, Julien Nabet, Szilárd Páll, Andrea Pasquadibisceglie, Michele Pellegrino, Nicola Piasentin, Daniele Rapetti, Muhammad Umair Sadiq, Hubert Santuz, Roland Schulz, Michael Shirts, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermühle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Cathrine Bergh, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/texindex.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/download.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/links.dat /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/api/gmxlibs.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/api/gmxlibs.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/api/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/api/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/gitlab-ci.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/gitlab-ci.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/language-features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/naming.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/reportstyle.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/style.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/testutils.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/code-formatting.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/code-formatting.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/fragments/doxygen-links.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/how-to/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/how-to/beginners.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/how-to/topology.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/how-to/topology.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/how-to/special.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/how-to/visualize.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/how-to/visualize.rst [ 8%] Built target thread_mpi /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/install-guide/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/install-guide/index.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/install-guide/exotic.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/install-guide/exotic.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/GMX_logos/gmx_logo_blue.svg /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/GMX_logos/gmx_logo_blue.svg cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2025/major/api.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2025/major/api.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/2024.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/2024.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2024/major/api.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2024/major/api.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/major/api.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/major/api.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/2022.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2022/major/api.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/major/api.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.7.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.7.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/2021.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/2021.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2021/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2021/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/2020.7.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/2020.7.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/removed-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/removed-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/deprecated-functionality.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/deprecated-functionality.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.7.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.7.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.6.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/2018.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/2018.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/removed-features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/removed-features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/portability.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/portability.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2018/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2018/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/2016.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/2016.5.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/2016.4.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/2016.4.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/2016.3.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/2016.3.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/2016.2.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/2016.2.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/2016.1.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/2016.1.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/highlights.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/highlights.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/new-features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/new-features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/tools.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/removed-features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/removed-features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/older/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/older/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/cmdline.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/cmdline.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/deprecation-policy.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/deprecation-policy.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/environment-variables.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/environment-variables.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/faq.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/faq.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/floating-point.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/floating-point.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/flow.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/flow.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/force-fields.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/force-fields.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/getting-started.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/getting-started.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/known-issues.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/known-issues.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/managing-simulations.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/managing-simulations.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/mdp-options.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/mdrun-features.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/mdrun-features.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/mdrun-performance.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/run-time-errors.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/run-time-errors.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/security.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/security.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 8%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/system-preparation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/system-preparation.rst make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/user-guide/terminology.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/user-guide/terminology.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/gmxapi/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/gmxapi/userguide/install.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/install.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/gmxapi/userguide/usage.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/gmxapi/userguide/pythonreference.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/pythonreference.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/nblib/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/nblib/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/nblib/guide-to-writing-MD-programs.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/nblib/guide-to-writing-MD-programs.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/preface.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/introduction.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/introduction.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/definitions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/definitions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/topologies.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/topologies.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/particle-type.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/parameter-files.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/parameter-files.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/molecule-definition.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/constraint-algorithm-section.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/constraint-algorithm-section.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/pdb2gmx-input-files.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/topology-file-formats.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/topologies/force-field-organization.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/topologies/force-field-organization.rst [ 8%] Built target linearalgebra cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/file-formats.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/file-formats.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/run-parameters.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/run-parameters.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/details.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/details.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/averages.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/averages.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/references.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/references.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/GMX_logos/gmx_falcon_blue.png /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/GMX_logos/gmx_falcon_blue.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/plotje.png /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/plotje.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/xvgr.png /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/xvgr.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/algorithms.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/algorithms.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/periodic-boundary-conditions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/periodic-boundary-conditions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/group-concept.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/group-concept.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/molecular-dynamics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/molecular-dynamics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/shell-molecular-dynamics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/shell-molecular-dynamics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/constraint-algorithms.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/constraint-algorithms.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/simulated-annealing.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/simulated-annealing.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/stochastic-dynamics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/stochastic-dynamics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/brownian-dynamics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/brownian-dynamics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/energy-minimization.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/energy-minimization.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/normal-mode-analysis.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/normal-mode-analysis.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/free-energy-calculations.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/free-energy-calculations.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/replica-exchange.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/replica-exchange.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/essential-dynamics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/essential-dynamics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/expanded-ensemble.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/expanded-ensemble.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/parallelization-domain-decomp.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/parallelization-domain-decomp.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/functions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/functions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/bonded-interactions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/bonded-interactions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/force-field.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/force-field.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/free-energy-interactions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/free-energy-interactions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/interaction-methods.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/interaction-methods.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/long-range-electrostatics.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/long-range-electrostatics.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/long-range-vdw.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/long-range-vdw.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/nonbonded-interactions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/nonbonded-interactions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/polarization.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/polarization.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/restraints.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/restraints.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/special.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/special.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/free-energy-implementation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/free-energy-implementation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/pulling.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/pulling.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/awh.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/awh.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/enforced-rotation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/enforced-rotation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/electric-fields.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/electric-fields.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/comp-electrophys.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/comp-electrophys.rst [ 8%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/free-energy-pmf.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/free-energy-pmf.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/remove-fast-dgf.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/remove-fast-dgf.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/viscosity-calculation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/viscosity-calculation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/shearing.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/shearing.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/tabulated-interaction-functions.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/tabulated-interaction-functions.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/qmmm.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/qmmm.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/vmd-imd.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/vmd-imd.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/membrane-embedding.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/membrane-embedding.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/mimic-qmmm.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/mimic-qmmm.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/density-guided-simulation.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/density-guided-simulation.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/colvars.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/colvars.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plumed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plumed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/nnpot.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/nnpot.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/analysis.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/analysis.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/using-groups.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/using-groups.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/looking-at-trajectory.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/looking-at-trajectory.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/general-properties.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/general-properties.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/radial-distribution-function.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/radial-distribution-function.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/correlation-function.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/correlation-function.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/curve-fitting.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/curve-fitting.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/mean-square-displacement.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/mean-square-displacement.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/bond-angle-dihedral.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/bond-angle-dihedral.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/radius-of-gyration.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/radius-of-gyration.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/rmsd.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/rmsd.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/covariance-analysis.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/covariance-analysis.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/dihedral-pca.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/dihedral-pca.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/hydrogen-bonds.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/hydrogen-bonds.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/protein-related.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/protein-related.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/interface-related.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/interface-related.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/decomp.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/decomp.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/dih.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/dih.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/drift-all.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/drift-all.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-angle.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/f-angle.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-bond.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/f-bond.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/fp-highres.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/fp-highres.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/int-mat.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/int-mat.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/mdpar.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/mdpar.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/parsort.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/parsort.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/ring.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/ring.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -MF CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserBytecode.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/shiftf.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/plots/shiftf.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/dd-cells.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/dd-cells.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/dd-tric.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/dd-tric.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/flowchart.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/flowchart.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free1.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/free1.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free2.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/free2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/leapfrog.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/leapfrog.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/lincs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/lincs.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/maxwell.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/maxwell.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/mpmd-pme.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/mpmd-pme.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/nstric.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/nstric.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/par-lincs2.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/par-lincs2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/pbctric.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/pbctric.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/rhododec.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/rhododec.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/truncoct.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/truncoct.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/verlet-drift.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/verlet-drift.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/angle.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/angle.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/bstretch.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/bstretch.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/chain.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/chain.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/dummies.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/dummies.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-bham.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-bham.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fbposres.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fbposres.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-dih.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-dih.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-dr.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-dr.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fig-02.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fig-02.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/fig-04.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fig-04.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-imps.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-imps.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-lj.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-lj.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-morse.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-morse.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-pr.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-pr.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/f-rbs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-rbs.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/ring-imp.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/ring-imp.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/softcore.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/softcore.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/gapsys-sc.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/gapsys-sc.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/subst-im.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/subst-im.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/tetra-im.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/tetra-im.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vcrf.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vcrf.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vsite-4fdn.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vsite-4fdn.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-invN.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-invN.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-pmfs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-pmfs.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-sampleweights.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-sampleweights.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-traj.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-traj.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/compelsetup.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/compelsetup.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/dumaro.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/dumaro.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 10%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/dumtypes.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/dumtypes.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/equipotential.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/equipotential.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/field.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/field.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/gaussians.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/gaussians.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/lambda-values.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/lambda-values.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pulldirrel.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/pulldirrel.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pull.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/pull.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pullref.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/pullref.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/rotation.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/rotation.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/dih-def.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/dih-def.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/distm.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/distm.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hbond-insert.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hbond-insert.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hbond.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hbond.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/hpr-wheel.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hpr-wheel.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/msdwater.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/msdwater.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/phipsi.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/phipsi.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rama.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rama.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rdfO-O.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdfO-O.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/rdf.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdf.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input-rst-timestamp.txt cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 33%] Built target sphinx-input-rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -MF CMakeFiles/muparser.dir/src/muParserCallback.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserCallback.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -MF CMakeFiles/muparser.dir/src/muParserDLL.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserDLL.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserError.cpp.o -MF CMakeFiles/muparser.dir/src/muParserError.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserError.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserError.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 33%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserInt.cpp.o -MF CMakeFiles/muparser.dir/src/muParserInt.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserInt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserInt.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -MF CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/muparser/src/muParserTokenReader.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 35%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,--dependency-file=CMakeFiles/muparser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 36%] Built target muparser /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 38%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/modularsimulator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/h5md_low_level_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,"\$ORIGIN/../lib:/usr/lib/aarch64-linux-gnu/openmpi/lib" -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm ../../lib/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.10.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/documentation/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.10.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/documentation/lib cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/launch_0_2_1.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/module.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_tprfile.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_no_gromacs_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file=CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-313-aarch64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -Wl,-rpath,/build/reproducible-path/gromacs-2025.0/build/documentation/lib:/usr/lib/aarch64-linux-gnu/openmpi/lib ../../lib/libgmxapi.so.0.4.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/documentation/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input && /usr/bin/cmake -E make_directory onlinehelp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input && /build/reproducible-path/gromacs-2025.0/build/documentation/bin/gmx -quiet help -export rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual && /usr/bin/sphinx-build -q -b latex -w sphinx-latex.log -d /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/_latex_doctrees -t do_latex /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.0/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run [ref.any] cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./gromacs.tex LaTeX2e <2024-11-01> patch level 1 L3 programming layer <2024-12-25> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (./sphinxpackagefootnote.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (./here.sty) (./picins.sty Option `picins' Version 3.0 Sep. 1992, TH Darmstadt/HRZ) (./underscore.sty) ==> First Aid for underscore.sty no longer applied! Expected: 2006/09/13 but found: 2001/10/12 so I'm assuming it got fixed. (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/dcolumn.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape.sty (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape-nometadata.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/lscape.sty))) Writing index file gromacs.idx (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) LaTeX Warning: Unused global option(s): [11]. No file gromacs.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc} <./gmx_falcon_blue.png>] No file gromacs.toc. [1] [1] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] Chapter 2. LaTeX Warning: Hyper reference `install-guide/index:cuda-gpu-acceleration' on p age 3 undefined on input line 178. LaTeX Warning: Reference `install-guide/index:cuda-gpu-acceleration' on page 3 undefined on input line 178. LaTeX Warning: Hyper reference `install-guide/index:sycl-gpu-acceleration-amd' on page 3 undefined on input line 179. LaTeX Warning: Reference `install-guide/index:sycl-gpu-acceleration-amd' on pag e 3 undefined on input line 179. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] LaTeX Warning: Hyper reference `install-guide/index:cuda-gpu-acceleration' on p age 4 undefined on input line 233. LaTeX Warning: Reference `install-guide/index:cuda-gpu-acceleration' on page 4 undefined on input line 233. Underfull \hbox (badness 5105) in paragraph at lines 303--311 \T1/pcr/m/n/10 CXX_-FLAGS\T1/ptm/m/n/10 . A clang com-piler is re-quired with v er-sion >=19. If you want to check which [4] LaTeX Warning: Hyper reference `install-guide/index:cmake-options' on page 5 un defined on input line 395. LaTeX Warning: Reference `install-guide/index:cmake-options' on page 5 undefine d on input line 395. LaTeX Warning: Hyper reference `install-guide/index:compiler' on page 5 undefin ed on input line 400. LaTeX Warning: Reference `install-guide/index:compiler' on page 5 undefined on input line 400. LaTeX Warning: Hyper reference `install-guide/index:compiler' on page 5 undefin ed on input line 404. LaTeX Warning: Reference `install-guide/index:compiler' on page 5 undefined on input line 404. LaTeX Warning: Hyper reference `install-guide/index:id1' on page 5 undefined on input line 408. LaTeX Warning: Reference `install-guide/index:id1' on page 5 undefined on input line 408. LaTeX Warning: Hyper reference `install-guide/index:simd-support' on page 5 und efined on input line 428. LaTeX Warning: Reference `install-guide/index:simd-support' on page 5 undefined on input line 428. LaTeX Warning: Hyper reference `install-guide/index:search-for-libraries-header s-or-programs' on page 5 undefined on input line 436. LaTeX Warning: Reference `install-guide/index:search-for-libraries-headers-or-p rograms' on page 5 undefined on input line 436. [5] LaTeX Warning: Hyper reference `install-guide/index:non-standard-location' on p age 6 undefined on input line 440. LaTeX Warning: Reference `install-guide/index:non-standard-location' on page 6 undefined on input line 440. LaTeX Warning: Hyper reference `install-guide/exotic:install-guide-static-linki ng' on page 6 undefined on input line 444. LaTeX Warning: Reference `install-guide/exotic:install-guide-static-linking' on page 6 undefined on input line 444. LaTeX Warning: Hyper reference `install-guide/index:fft-support' on page 6 unde fined on input line 448. LaTeX Warning: Reference `install-guide/index:fft-support' on page 6 undefined on input line 448. LaTeX Warning: Hyper reference `user-guide/known-issues:gmx-users-known-issues' on page 6 undefined on input line 518. LaTeX Warning: Reference `user-guide/known-issues:gmx-users-known-issues' on pa ge 6 undefined on input line 518. [6] LaTeX Warning: Hyper reference `install-guide/index:cuda-gpu-acceleration' on p age 7 undefined on input line 653. LaTeX Warning: Reference `install-guide/index:cuda-gpu-acceleration' on page 7 undefined on input line 653. [7] LaTeX Warning: Hyper reference `install-guide/index:opencl-gpu-acceleration' on page 8 undefined on input line 692. LaTeX Warning: Reference `install-guide/index:opencl-gpu-acceleration' on page 8 undefined on input line 692. LaTeX Warning: Hyper reference `install-guide/index:sycl-gpu-acceleration-intel ' on page 8 undefined on input line 746. LaTeX Warning: Reference `install-guide/index:sycl-gpu-acceleration-intel' on p age 8 undefined on input line 746. LaTeX Warning: Hyper reference `install-guide/index:sycl-gpu-acceleration-amd' on page 8 undefined on input line 746. LaTeX Warning: Reference `install-guide/index:sycl-gpu-acceleration-amd' on pag e 8 undefined on input line 746. LaTeX Warning: Hyper reference `install-guide/index:amd-hip' on page 8 undefine d on input line 790. LaTeX Warning: Reference `install-guide/index:amd-hip' on page 8 undefined on i nput line 790. [8] Underfull \hbox (badness 10000) in paragraph at lines 881--886 []\T1/ptm/m/n/10 Sup-port for this fea-ture in GRO-MACS is cur-rently en-abled by build-ing with NVSH-MEM Underfull \hbox (badness 10000) in paragraph at lines 881--886 \T1/ptm/m/n/10 sup-port (\T1/pcr/m/n/10 GMX_-NVSHMEM=ON\T1/ptm/m/n/10 ) and spe c-i-fy-ing the NVSH-MEM root di-rec-tory (\T1/pcr/m/n/10 NVSHMEM_- [9] LaTeX Warning: Hyper reference `install-guide/index:linear-algebra-libraries' o n page 10 undefined on input line 917. LaTeX Warning: Reference `install-guide/index:linear-algebra-libraries' on page 10 undefined on input line 917. [10] [11] LaTeX Warning: Hyper reference `install-guide/index:amd-hip' on page 12 undefin ed on input line 1128. LaTeX Warning: Reference `install-guide/index:amd-hip' on page 12 undefined on input line 1128. LaTeX Warning: Hyper reference `install-guide/index:linear-algebra-libraries' o n page 12 undefined on input line 1165. LaTeX Warning: Reference `install-guide/index:linear-algebra-libraries' on page 12 undefined on input line 1165. [12] LaTeX Warning: Hyper reference `install-guide/index:cmake' on page 13 undefined on input line 1215. LaTeX Warning: Reference `install-guide/index:cmake' on page 13 undefined on in put line 1215. [13] [14] [15] [16] LaTeX Warning: Hyper reference `install-guide/exotic:install-guide-exotic-sycl' on page 17 undefined on input line 1747. LaTeX Warning: Reference `install-guide/exotic:install-guide-exotic-sycl' on pa ge 17 undefined on input line 1747. [17] LaTeX Warning: Hyper reference `install-guide/index:bbfft-installation' on page 18 undefined on input line 1797. LaTeX Warning: Reference `install-guide/index:bbfft-installation' on page 18 un defined on input line 1797. LaTeX Warning: Hyper reference `install-guide/exotic:install-guide-exotic-sycl' on page 18 undefined on input line 1849. LaTeX Warning: Reference `install-guide/exotic:install-guide-exotic-sycl' on pa ge 18 undefined on input line 1849. [18] LaTeX Warning: Hyper reference `install-guide/exotic:install-guide-static-linki ng' on page 19 undefined on input line 1935. LaTeX Warning: Reference `install-guide/exotic:install-guide-static-linking' on page 19 undefined on input line 1935. [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2092--2094 [][]\T1/pcr/m/n/10 DGMX_-FFT_-LIBRARY= []DFFTWF_-LIBRA RY=, but at most version <1.5> allowed [28] [29 <./graphviz-546f8676b043be7a824d2ab2320a5e60473f82fc.pdf>] LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 30 undefined on input line 2830. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 30 undefined on input line 2830. LaTeX Warning: Hyper reference `user-guide/flow::doc' on page 30 undefined on i nput line 2836. LaTeX Warning: Reference `user-guide/flow::doc' on page 30 undefined on input l ine 2836. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 30 undefined on input line 2849. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 30 undefi ned on input line 2849. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 30 undefined on input line 2850. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 30 undefi ned on input line 2850. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 30 u ndefined on input line 2850. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 30 undefin ed on input line 2850. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 30 u ndefined on input line 2859. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 30 undefin ed on input line 2859. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-include' on page 30 undefined on input line 2869. LaTeX Warning: Reference `user-guide/mdp-options:mdp-include' on page 30 undefi ned on input line 2869. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 30 u ndefined on input line 2869. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 30 undefin ed on input line 2869. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 30 u ndefined on input line 2890. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 30 undefin ed on input line 2890. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 30 u ndefined on input line 2894. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 30 undefin ed on input line 2894. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 30 u ndefined on input line 2895. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 30 undefin ed on input line 2895. [30] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 31 undefined on input line 2902. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 31 undefi ned on input line 2902. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 31 u ndefined on input line 2903. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 31 undefin ed on input line 2903. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 31 u ndefined on input line 2904. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 31 undefin ed on input line 2904. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 31 u ndefined on input line 2904. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 31 undefin ed on input line 2904. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 31 u ndefined on input line 2905. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 31 undefin ed on input line 2905. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 31 u ndefined on input line 2907. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 31 undefin ed on input line 2907. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefined on input line 2908. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefi ned on input line 2908. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 3 1 undefined on input line 2909. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 31 unde fined on input line 2909. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefined on input line 2910. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefi ned on input line 2910. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefined on input line 2912. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefi ned on input line 2912. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefined on input line 2913. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 31 undefi ned on input line 2913. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 31 undefined on input line 2914. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 31 undefi ned on input line 2914. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 31 u ndefined on input line 2921. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 31 undefin ed on input line 2921. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 31 u ndefined on input line 2924. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 31 undefin ed on input line 2924. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 31 u ndefined on input line 2939. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 31 undefin ed on input line 2939. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 31 u ndefined on input line 2940. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 31 undefin ed on input line 2940. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 31 u ndefined on input line 2940. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 31 undefin ed on input line 2940. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 31 u ndefined on input line 2941. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 31 undefin ed on input line 2941. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 31 u ndefined on input line 2941. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 31 undefin ed on input line 2941. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 31 un defined on input line 2943. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 31 undefine d on input line 2943. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 31 u ndefined on input line 2944. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 31 undefin ed on input line 2944. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 unde fined on input line 2951. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 undefined on input line 2951. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 unde fined on input line 2952. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 undefined on input line 2952. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 31 u ndefined on input line 2954. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 31 undefin ed on input line 2954. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 unde fined on input line 2954. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 31 undefined on input line 2954. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 31 u ndefined on input line 2955. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 31 undefin ed on input line 2955. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 31 u ndefined on input line 2955. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 31 undefin ed on input line 2955. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 31 u ndefined on input line 2956. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 31 undefin ed on input line 2956. LaTeX Warning: Hyper reference `how-to/index::doc' on page 31 undefined on inpu t line 2964. LaTeX Warning: Reference `how-to/index::doc' on page 31 undefined on input line 2964. [31] LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 32 undefined on input line 3062. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 32 undefi ned on input line 3062. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 32 undefined on input line 3063. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 32 undefined on input line 3063. LaTeX Warning: Hyper reference `onlinehelp/gmx-genconf:gmx-genconf' on page 32 undefined on input line 3063. LaTeX Warning: Reference `onlinehelp/gmx-genconf:gmx-genconf' on page 32 undefi ned on input line 3063. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 32 undefined on input line 3069. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 32 undefi ned on input line 3069. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 32 unde fined on input line 3069. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 32 undefined on input line 3069. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 32 undefined on input line 3070. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 32 u ndefined on input line 3070. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 3 2 undefined on input line 3077. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 32 unde fined on input line 3077. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 32 undefined on input line 3079. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 32 undefi ned on input line 3079. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 un defined on input line 3080. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 undefine d on input line 3080. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 32 undefined on input line 3080. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 32 undefined on input line 3080. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 un defined on input line 3087. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 undefine d on input line 3087. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 32 unde fined on input line 3088. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 32 undefined on input line 3088. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 32 u ndefined on input line 3100. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 32 undefin ed on input line 3100. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 32 u ndefined on input line 3108. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 32 undefin ed on input line 3108. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 un defined on input line 3117. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 32 undefine d on input line 3117. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 32 unde fined on input line 3118. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 32 undefined on input line 3118. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 32 un defined on input line 3118. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 32 undefine d on input line 3118. LaTeX Warning: Hyper reference `how-to/visualize::doc' on page 32 undefined on input line 3118. LaTeX Warning: Reference `how-to/visualize::doc' on page 32 undefined on input line 3118. [32] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 33 u ndefined on input line 3123. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 33 undefin ed on input line 3123. LaTeX Warning: Hyper reference `user-guide/cmdline::doc' on page 33 undefined o n input line 3139. LaTeX Warning: Reference `user-guide/cmdline::doc' on page 33 undefined on inpu t line 3139. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3159. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3159. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 33 u ndefined on input line 3165. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 33 undefin ed on input line 3165. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 33 u ndefined on input line 3166. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 33 undefin ed on input line 3166. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3171. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3171. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3172. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3172. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3172. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3172. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3178. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3178. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsteps' on page 33 u ndefined on input line 3182. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsteps' on page 33 undefin ed on input line 3182. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 unde fined on input line 3194. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 33 undefined on input line 3194. LaTeX Warning: Hyper reference `onlinehelp/gmx-check:gmx-check' on page 33 unde fined on input line 3218. LaTeX Warning: Reference `onlinehelp/gmx-check:gmx-check' on page 33 undefined on input line 3218. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 33 undefi ned on input line 3219. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 33 undefined on input line 3219. [33] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 34 unde fined on input line 3225. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 34 undefined on input line 3225. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-simulation-part' on page 34 undefined on input line 3240. LaTeX Warning: Reference `user-guide/mdp-options:mdp-simulation-part' on page 3 4 undefined on input line 3240. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 un defined on input line 3241. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 undefine d on input line 3241. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 34 unde fined on input line 3259. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 34 undefined on input line 3259. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 34 u ndefined on input line 3272. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 34 undefin ed on input line 3272. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 34 undefined on input line 3273. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 3 4 undefined on input line 3273. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 34 u ndefined on input line 3282. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 34 undefin ed on input line 3282. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 un defined on input line 3283. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 undefine d on input line 3283. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 34 u ndefined on input line 3291. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 34 undefin ed on input line 3291. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 un defined on input line 3300. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 34 undefine d on input line 3300. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 34 u ndefined on input line 3301. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 34 undefin ed on input line 3301. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tinit' on page 34 un defined on input line 3302. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tinit' on page 34 undefine d on input line 3302. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-step' on page 3 4 undefined on input line 3302. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-step' on page 34 unde fined on input line 3302. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsteps' on page 34 u ndefined on input line 3303. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsteps' on page 34 undefin ed on input line 3303. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-simulation-part' on page 34 undefined on input line 3303. LaTeX Warning: Reference `user-guide/mdp-options:mdp-simulation-part' on page 3 4 undefined on input line 3303. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-gen-vel' on page 34 undefined on input line 3304. LaTeX Warning: Reference `user-guide/mdp-options:mdp-gen-vel' on page 34 undefi ned on input line 3304. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-continuation' on pag e 34 undefined on input line 3305. LaTeX Warning: Reference `user-guide/mdp-options:mdp-continuation' on page 34 u ndefined on input line 3305. [34] [35] LaTeX Warning: Hyper reference `onlinehelp/gmx-pme_error:gmx-pme-error' on page 36 undefined on input line 3458. LaTeX Warning: Reference `onlinehelp/gmx-pme_error:gmx-pme-error' on page 36 un defined on input line 3458. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 36 unde fined on input line 3459. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 36 undefined on input line 3459. LaTeX Warning: Hyper reference `install-guide/index:mpi-support' on page 36 und efined on input line 3459. LaTeX Warning: Reference `install-guide/index:mpi-support' on page 36 undefined on input line 3459. LaTeX Warning: Hyper reference `install-guide/index:configure-cmake' on page 36 undefined on input line 3461. LaTeX Warning: Reference `install-guide/index:configure-cmake' on page 36 undef ined on input line 3461. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 36 unde fined on input line 3462. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 36 undefined on input line 3462. LaTeX Warning: Hyper reference `install-guide/index:gmx-special-build' on page 36 undefined on input line 3475. LaTeX Warning: Reference `install-guide/index:gmx-special-build' on page 36 und efined on input line 3475. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 36 undefined on input line 3485. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 36 undefined on input line 3485. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefined on input line 3485. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefi ned on input line 3485. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 36 undefined on input line 3488. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 36 undefined on input line 3488. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefined on input line 3490. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefi ned on input line 3490. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefined on input line 3492. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefi ned on input line 3492. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 36 un defined on input line 3494. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 36 undefine d on input line 3494. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefined on input line 3499. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 36 undefi ned on input line 3499. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 36 u ndefined on input line 3504. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 36 undefin ed on input line 3504. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 36 u ndefined on input line 3506. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 36 undefin ed on input line 3506. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 36 u ndefined on input line 3522. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 36 undefin ed on input line 3522. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 36 u ndefined on input line 3523. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 36 undefin ed on input line 3523. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 36 u ndefined on input line 3530. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 36 undefin ed on input line 3530. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 36 u ndefined on input line 3533. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 36 undefin ed on input line 3533. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 36 undefined on input line 3533. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 36 undefined on input line 3533. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 36 u ndefined on input line 3535. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 36 undefin ed on input line 3535. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-need-for-gro' on page 36 undefined on input line 3535. LaTeX Warning: Reference `user-guide/getting-started:gmx-need-for-gro' on page 36 undefined on input line 3535. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 36 u ndefined on input line 3536. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 36 undefin ed on input line 3536. [36] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 37 undefined on input line 3540. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 37 undefi ned on input line 3540. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 37 u ndefined on input line 3540. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 37 undefin ed on input line 3540. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 37 u ndefined on input line 3543. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 37 undefin ed on input line 3543. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 37 u ndefined on input line 3543. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 37 undefin ed on input line 3543. LaTeX Warning: Hyper reference `user-guide/system-preparation::doc' on page 37 undefined on input line 3546. LaTeX Warning: Reference `user-guide/system-preparation::doc' on page 37 undefi ned on input line 3546. LaTeX Warning: Hyper reference `user-guide/run-time-errors:gmx-atom-missing' on page 37 undefined on input line 3554. LaTeX Warning: Reference `user-guide/run-time-errors:gmx-atom-missing' on page 37 undefined on input line 3554. LaTeX Warning: Hyper reference `user-guide/floating-point:gmx-floating-point' o n page 37 undefined on input line 3565. LaTeX Warning: Reference `user-guide/floating-point:gmx-floating-point' on page 37 undefined on input line 3565. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-thermostats' on page 37 undefined on input line 3583. LaTeX Warning: Reference `user-guide/terminology:gmx-thermostats' on page 37 un defined on input line 3583. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-thermostats-dont' on page 37 undefined on input line 3584. LaTeX Warning: Reference `user-guide/terminology:gmx-thermostats-dont' on page 37 undefined on input line 3584. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tinit' on page 37 un defined on input line 3592. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tinit' on page 37 undefine d on input line 3592. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-step' on page 3 7 undefined on input line 3592. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-step' on page 37 unde fined on input line 3592. LaTeX Warning: Hyper reference `onlinehelp/gmx-genrestr:gmx-genrestr' on page 3 7 undefined on input line 3611. LaTeX Warning: Reference `onlinehelp/gmx-genrestr:gmx-genrestr' on page 37 unde fined on input line 3611. LaTeX Warning: Hyper reference `user-guide/managing-simulations:managing-long-s imulations' on page 37 undefined on input line 3618. LaTeX Warning: Reference `user-guide/managing-simulations:managing-long-simulat ions' on page 37 undefined on input line 3618. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 37 u ndefined on input line 3619. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 37 undefin ed on input line 3619. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 37 u ndefined on input line 3620. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 37 undefin ed on input line 3620. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 37 undefined on input line 3620. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 3 7 undefined on input line 3620. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 37 unde fined on input line 3627. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 37 undefined on input line 3627. LaTeX Warning: Hyper reference `user-guide/mdrun-features:single-point-energy' on page 37 undefined on input line 3628. LaTeX Warning: Reference `user-guide/mdrun-features:single-point-energy' on pag e 37 undefined on input line 3628. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-md' on page 37 undef ined on input line 3644. LaTeX Warning: Reference `user-guide/terminology:gmx-md' on page 37 undefined o n input line 3644. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 37 undefined on input line 3648. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 37 un defined on input line 3648. [37] LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 38 undefined on input line 3659. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 38 un defined on input line 3659. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 38 u ndefined on input line 3677. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 38 undefin ed on input line 3677. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 38 u ndefined on input line 3679. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 38 undefin ed on input line 3679. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 38 un defined on input line 3680. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 38 undefine d on input line 3680. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-pbc' on page 38 unde fined on input line 3688. LaTeX Warning: Reference `user-guide/terminology:gmx-pbc' on page 38 undefined on input line 3688. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 38 undefined on input line 3689. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 38 undefi ned on input line 3689. LaTeX Warning: Hyper reference `user-guide/floating-point:gmx-floating-point' o n page 38 undefined on input line 3697. LaTeX Warning: Reference `user-guide/floating-point:gmx-floating-point' on page 38 undefined on input line 3697. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 38 undefined on input line 3712. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 38 un defined on input line 3712. [38] LaTeX Warning: Hyper reference `user-guide/terminology:gmx-md' on page 39 undef ined on input line 3778. LaTeX Warning: Reference `user-guide/terminology:gmx-md' on page 39 undefined o n input line 3778. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 39 undefined on input line 3779. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 39 un defined on input line 3779. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 39 u ndefined on input line 3784. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 39 undefin ed on input line 3784. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 39 undefined on input line 3837. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 39 un defined on input line 3837. [39] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 40 u ndefined on input line 3887. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 40 undefin ed on input line 3887. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 40 u ndefined on input line 3918. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 40 undefin ed on input line 3918. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-ste ep' on page 40 undefined on input line 3946. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-steep' on page 40 undefined on input line 3946. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 40 undefined on input line 3974. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 40 undefined on input line 3974. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 40 undefined on input line 3982. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 40 undefined on input line 3982. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv' on page 40 undefined on input line 3997. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv' on page 40 undefined on input line 3997. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 40 undefined on input line 3999. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 40 undefined on input line 3999. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tc-grps' on page 40 undefined on input line 4020. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tc-grps' on page 40 undefi ned on input line 4020. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-t' on page 40 un defined on input line 4021. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-t' on page 40 undefine d on input line 4021. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 40 un defined on input line 4022. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 40 undefine d on input line 4022. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tcoupl' on page 40 u ndefined on input line 4022. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tcoupl' on page 40 undefin ed on input line 4022. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 40 undefined on input line 4022. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 40 und efined on input line 4022. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 40 undefined on input line 4024. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 40 undefi ned on input line 4024. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 40 un defined on input line 4025. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 40 undefine d on input line 4025. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 40 un defined on input line 4029. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 40 undefine d on input line 4029. [40] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-bd-fric' on page 41 undefined on input line 4044. LaTeX Warning: Reference `user-guide/mdp-options:mdp-bd-fric' on page 41 undefi ned on input line 4044. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-t' on page 41 un defined on input line 4044. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-t' on page 41 undefine d on input line 4044. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-bd-fric' on page 41 undefined on input line 4045. LaTeX Warning: Reference `user-guide/mdp-options:mdp-bd-fric' on page 41 undefi ned on input line 4045. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 41 un defined on input line 4046. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 41 undefine d on input line 4046. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-sd' on page 41 undefined on input line 4047. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-sd' on pa ge 41 undefined on input line 4047. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 41 undefined on input line 4048. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 41 undefi ned on input line 4048. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-emstep' on page 41 u ndefined on input line 4062. LaTeX Warning: Reference `user-guide/mdp-options:mdp-emstep' on page 41 undefin ed on input line 4062. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-emtol' on page 41 un defined on input line 4063. LaTeX Warning: Reference `user-guide/mdp-options:mdp-emtol' on page 41 undefine d on input line 4063. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-emtol' on page 41 un defined on input line 4077. LaTeX Warning: Reference `user-guide/mdp-options:mdp-emtol' on page 41 undefine d on input line 4077. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcgsteep' on page 41 undefined on input line 4079. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcgsteep' on page 41 und efined on input line 4079. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 41 u ndefined on input line 4111. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 41 undefin ed on input line 4111. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsteps' on page 41 u ndefined on input line 4128. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsteps' on page 41 undefin ed on input line 4128. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefined on input line 4130. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefi ned on input line 4130. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefined on input line 4131. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefi ned on input line 4131. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rtpi' on page 41 und efined on input line 4132. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rtpi' on page 41 undefined on input line 4132. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 41 undefined on input line 4136. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 41 undefi ned on input line 4136. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-t' on page 41 un defined on input line 4137. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-t' on page 41 undefine d on input line 4137. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-tpi ' on page 41 undefined on input line 4160. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-tpi' on p age 41 undefined on input line 4160. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rtpi' on page 41 und efined on input line 4165. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rtpi' on page 41 undefined on input line 4165. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefined on input line 4167. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 41 undefi ned on input line 4167. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-tpi c' on page 41 undefined on input line 4168. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-tpic' on page 41 undefined on input line 4168. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-tpi c' on page 41 undefined on input line 4169. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-tpic' on page 41 undefined on input line 4169. [41] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-QMMM-grps' on page 4 2 undefined on input line 4188. LaTeX Warning: Reference `user-guide/mdp-options:mdp-QMMM-grps' on page 42 unde fined on input line 4188. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tinit' on page 42 un defined on input line 4251. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tinit' on page 42 undefine d on input line 4251. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-dt' on page 42 undef ined on input line 4251. LaTeX Warning: Reference `user-guide/mdp-options:mdp-dt' on page 42 undefined o n input line 4251. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-step' on page 4 2 undefined on input line 4252. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-step' on page 42 unde fined on input line 4252. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda' on page 42 undefined on input line 4253. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda' on page 42 un defined on input line 4253. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-delta-lambda' on pag e 42 undefined on input line 4253. LaTeX Warning: Reference `user-guide/mdp-options:mdp-delta-lambda' on page 42 u ndefined on input line 4253. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-step' on page 4 2 undefined on input line 4254. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-step' on page 42 unde fined on input line 4254. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-step' on page 4 2 undefined on input line 4256. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-step' on page 42 unde fined on input line 4256. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 42 undefined on input line 4257. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 4 2 undefined on input line 4257. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-mts-level2-forces' o n page 42 undefined on input line 4310. LaTeX Warning: Reference `user-guide/mdp-options:mdp-mts-level2-forces' on page 42 undefined on input line 4310. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-mts-level2-factor' o n page 42 undefined on input line 4310. LaTeX Warning: Reference `user-guide/mdp-options:mdp-mts-level2-factor' on page 42 undefined on input line 4310. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 42 undefined on input line 4312. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 42 undefined on input line 4312. Underfull \hbox (badness 10000) in paragraph at lines 4307--4313 \T1/ptm/m/n/10 Use a mul-ti-ple timing-stepping in-te-gra-tor to eval-u-ate som e forces, as spec-i-fied by LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-mts-level2-factor' o n page 42 undefined on input line 4345. LaTeX Warning: Reference `user-guide/mdp-options:mdp-mts-level2-factor' on page 42 undefined on input line 4345. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-constraints-h- bonds' on page 42 undefined on input line 4387. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-constraints-h-bonds' on page 42 undefined on input line 4387. [42] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcomm' on page 43 undefined on input line 4435. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcomm' on page 43 undefi ned on input line 4435. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcomm' on page 43 undefined on input line 4437. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcomm' on page 43 undefi ned on input line 4437. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-bd-fric' on page 43 undefined on input line 4500. LaTeX Warning: Reference `user-guide/mdp-options:mdp-bd-fric' on page 43 undefi ned on input line 4500. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 43 un defined on input line 4502. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 43 undefine d on input line 4502. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 43 undefined on input line 4517. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 43 undefi ned on input line 4517. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 43 undefined on input line 4519. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 43 undefi ned on input line 4519. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-emtol' on page 43 un defined on input line 4594. LaTeX Warning: Reference `user-guide/mdp-options:mdp-emtol' on page 43 undefine d on input line 4594. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-niter' on page 43 un defined on input line 4595. LaTeX Warning: Reference `user-guide/mdp-options:mdp-niter' on page 43 undefine d on input line 4595. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-emtol' on page 43 un defined on input line 4596. LaTeX Warning: Reference `user-guide/mdp-options:mdp-emtol' on page 43 undefine d on input line 4596. [43] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-tpi ' on page 44 undefined on input line 4647. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-tpi' on p age 44 undefined on input line 4647. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-tpi c' on page 44 undefined on input line 4647. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-tpic' on page 44 undefined on input line 4647. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 44 u ndefined on input line 4665. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 44 undefin ed on input line 4665. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 44 u ndefined on input line 4682. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 44 undefin ed on input line 4682. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 44 u ndefined on input line 4699. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 44 undefin ed on input line 4699. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 44 u ndefined on input line 4749. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 44 undefin ed on input line 4749. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcalcenergy' on pa ge 44 undefined on input line 4750. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcalcenergy' on page 44 undefined on input line 4750. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcalcenergy' on pa ge 44 undefined on input line 4751. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcalcenergy' on page 44 undefined on input line 4751. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 44 un defined on input line 4752. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 44 undefine d on input line 4752. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstenergy' on page 4 4 undefined on input line 4753. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstenergy' on page 44 unde fined on input line 4753. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 44 u ndefined on input line 4768. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 44 undefin ed on input line 4768. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstxout-compressed' on page 44 undefined on input line 4798. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstxout-compressed' on pag e 44 undefined on input line 4798. [44] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-tolera nce' on page 45 undefined on input line 4836. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-tolerance' o n page 45 undefined on input line 4836. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 45 un defined on input line 4837. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 45 undefine d on input line 4837. Underfull \hbox (badness 5862) in paragraph at lines 4833--4839 \T1/ptm/m/n/10 Gen-er-ate a pair list with buffer-ing. The buffer size is au-to -mat-i-cally set based on LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-tolera nce' on page 45 undefined on input line 4885. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-tolerance' o n page 45 undefined on input line 4885. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 4885. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 4885. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 45 unde fined on input line 4886. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 45 undefined on input line 4886. Underfull \hbox (badness 10000) in paragraph at lines 4882--4892 \T1/ptm/m/n/10 In-ter-val be-tween steps that up-date the neigh-bor list. When dy-nam-ics and LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 4957. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 4957. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 4959. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 4959. LaTeX Warning: Hyper reference `user-guide/mdp-options:walls' on page 45 undefi ned on input line 4973. LaTeX Warning: Reference `user-guide/mdp-options:walls' on page 45 undefined on input line 4973. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 45 un defined on input line 5035. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 45 undefine d on input line 5035. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 5036. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 5036. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 5039. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 5039. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 45 un defined on input line 5041. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 45 undefine d on input line 5041. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefined on input line 5045. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 45 undefi ned on input line 5045. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-dt' on page 45 undef ined on input line 5045. LaTeX Warning: Reference `user-guide/mdp-options:mdp-dt' on page 45 undefined o n input line 5045. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-tolera nce' on page 45 undefined on input line 5058. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-tolerance' o n page 45 undefined on input line 5058. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 45 un defined on input line 5058. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 45 undefine d on input line 5058. [45] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-tolera nce' on page 46 undefined on input line 5075. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-tolerance' o n page 46 undefined on input line 5075. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 46 und efined on input line 5078. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 46 undefined on input line 5078. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-tolera nce' on page 46 undefined on input line 5098. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-tolerance' o n page 46 undefined on input line 5098. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-verlet-buffer-pressu re-tolerance' on page 46 undefined on input line 5099. LaTeX Warning: Reference `user-guide/mdp-options:mdp-verlet-buffer-pressure-tol erance' on page 46 undefined on input line 5099. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5100. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5100. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 46 un defined on input line 5104. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 46 undefine d on input line 5104. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5106. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5106. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5129. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5129. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undefined on input line 5130. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undef ined on input line 5130. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5130. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5130. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undefined on input line 5131. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undef ined on input line 5131. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-coulomb-modifier' on page 46 undefined on input line 5132. LaTeX Warning: Reference `user-guide/mdp-options:mdp-coulomb-modifier' on page 46 undefined on input line 5132. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undefined on input line 5150. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undef ined on input line 5150. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5150. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5150. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 46 un defined on input line 5151. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 46 undefine d on input line 5151. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undefined on input line 5151. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 46 undef ined on input line 5151. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fourierspacing' on p age 46 undefined on input line 5153. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fourierspacing' on page 46 undefined on input line 5153. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-rtol' on page 46 undefined on input line 5154. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-rtol' on page 46 und efined on input line 5154. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fourierspacing' on p age 46 undefined on input line 5175. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fourierspacing' on page 46 undefined on input line 5175. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pme-order' on page 4 6 undefined on input line 5176. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pme-order' on page 46 unde fined on input line 5176. [46] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undefined on input line 5212. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undef ined on input line 5212. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 47 un defined on input line 5212. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 47 undefine d on input line 5212. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 47 und efined on input line 5212. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 47 undefined on input line 5212. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-epsilon-rf' on page 47 undefined on input line 5214. LaTeX Warning: Reference `user-guide/mdp-options:mdp-epsilon-rf' on page 47 und efined on input line 5214. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-epsilon-rf' on page 47 undefined on input line 5215. LaTeX Warning: Reference `user-guide/mdp-options:mdp-epsilon-rf' on page 47 und efined on input line 5215. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 unde fined on input line 5229. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 undefined on input line 5229. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 unde fined on input line 5231. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 undefined on input line 5231. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-vdwtype' on page 47 undefined on input line 5238. LaTeX Warning: Reference `user-guide/mdp-options:mdp-vdwtype' on page 47 undefi ned on input line 5238. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-table-extension' on page 47 undefined on input line 5241. LaTeX Warning: Reference `user-guide/mdp-options:mdp-table-extension' on page 4 7 undefined on input line 5241. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undefined on input line 5262. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undef ined on input line 5262. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 47 un defined on input line 5263. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 47 undefine d on input line 5263. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undefined on input line 5278. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 47 undef ined on input line 5278. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 47 un defined on input line 5279. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 47 undefine d on input line 5279. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 unde fined on input line 5280. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 47 undefined on input line 5280. [47] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 48 unde fined on input line 5371. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 48 undefined on input line 5371. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 48 un defined on input line 5425. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 48 undefine d on input line 5425. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5426. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5426. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rlist' on page 48 un defined on input line 5426. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rlist' on page 48 undefine d on input line 5426. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5426. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5426. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fourierspacing' on p age 48 undefined on input line 5440. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fourierspacing' on page 48 undefined on input line 5440. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pme-order' on page 4 8 undefined on input line 5442. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pme-order' on page 48 unde fined on input line 5442. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-rtol-lj' on pa ge 48 undefined on input line 5443. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-rtol-lj' on page 48 undefined on input line 5443. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lj-pme-comb-rule' on page 48 undefined on input line 5445. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lj-pme-comb-rule' on page 48 undefined on input line 5445. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-vdwtype-Cut-of f' on page 48 undefined on input line 5459. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-vdwtype-Cut-off' on page 48 undefined on input line 5459. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-vdw-modifier-F orce-switch' on page 48 undefined on input line 5459. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-vdw-modifier-Force-s witch' on page 48 undefined on input line 5459. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 undefined on input line 5461. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 un defined on input line 5461. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5462. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5462. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-vdwtype-Cut-of f' on page 48 undefined on input line 5476. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-vdwtype-Cut-off' on page 48 undefined on input line 5476. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-vdw-modifier-P otential-switch' on page 48 undefined on input line 5476. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-vdw-modifier-Potenti al-switch' on page 48 undefined on input line 5476. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 undefined on input line 5477. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 un defined on input line 5477. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5478. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5478. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-coulombtype-Us er' on page 48 undefined on input line 5496. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-coulombtype-User' on page 48 undefined on input line 5496. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5498. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5498. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-coulombtype' on page 48 undefined on input line 5499. LaTeX Warning: Reference `user-guide/mdp-options:mdp-coulombtype' on page 48 un defined on input line 5499. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 undefined on input line 5553. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 un defined on input line 5553. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5554. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5554. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 undefined on input line 5572. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw-switch' on page 48 un defined on input line 5572. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 48 und efined on input line 5572. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 48 undefined on input line 5572. [48] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-energygrps' on page 49 undefined on input line 5695. LaTeX Warning: Reference `user-guide/mdp-options:mdp-energygrps' on page 49 und efined on input line 5695. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 unde fined on input line 5697. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 undefined on input line 5697. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fourier-nx' on page 49 undefined on input line 5723. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fourier-nx' on page 49 und efined on input line 5723. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 49 undefined on input line 5728. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 49 undef ined on input line 5728. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 unde fined on input line 5728. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 undefined on input line 5728. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fourierspacing' on p age 49 undefined on input line 5764. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fourierspacing' on page 49 undefined on input line 5764. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 49 undefined on input line 5766. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 49 undef ined on input line 5766. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 unde fined on input line 5767. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 49 undefined on input line 5767. [49] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 50 undefined on input line 5802. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 50 undef ined on input line 5802. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-rtol' on page 50 undefined on input line 5802. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-rtol' on page 50 und efined on input line 5802. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-rtol-lj' on pa ge 50 undefined on input line 5818. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-rtol-lj' on page 50 undefined on input line 5818. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 50 und efined on input line 5820. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 50 undefined on input line 5820. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-rtol' on page 50 undefined on input line 5820. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-rtol' on page 50 und efined on input line 5820. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 50 un defined on input line 5948. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 50 undefine d on input line 5948. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ensemble-temperature ' on page 50 undefined on input line 5966. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ensemble-temperature' on p age 50 undefined on input line 5966. [50] Underfull \hbox (badness 10000) in paragraph at lines 6013--6018 []\T1/ptm/m/n/10 The en-sem-ble tem-per-a-ture for the sys-tem. The in-put valu e is only used with LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-t' on page 51 un defined on input line 6051. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-t' on page 51 undefine d on input line 6051. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6052. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6052. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tc-grps' on page 51 undefined on input line 6053. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tc-grps' on page 51 undefi ned on input line 6053. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6071. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6071. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6089. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6089. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6108. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6108. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6126. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6126. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ld-seed' on page 51 undefined on input line 6128. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ld-seed' on page 51 undefi ned on input line 6128. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-t' on page 51 un defined on input line 6129. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-t' on page 51 undefine d on input line 6129. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 51 undefined on input line 6149. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 51 und efined on input line 6149. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 51 undefined on input line 6154. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 51 und efined on input line 6154. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 51 undefined on input line 6169. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 51 undefined on input line 6169. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 51 u ndefined on input line 6171. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 51 undefin ed on input line 6171. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-print-nose-hoover-ch ain-variables' on page 51 undefined on input line 6172. LaTeX Warning: Reference `user-guide/mdp-options:mdp-print-nose-hoover-chain-va riables' on page 51 undefined on input line 6172. [51] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tc-grps' on page 52 undefined on input line 6237. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tc-grps' on page 52 undefi ned on input line 6237. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tc-grps' on page 52 undefined on input line 6252. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tc-grps' on page 52 undefi ned on input line 6252. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 52 un defined on input line 6289. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 52 undefine d on input line 6289. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 52 undefined on input line 6289. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 52 und efined on input line 6289. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 52 un defined on input line 6307. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 52 undefine d on input line 6307. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 52 undefined on input line 6308. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 52 und efined on input line 6308. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 52 un defined on input line 6326. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 52 undefine d on input line 6326. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv' on page 52 undefined on input line 6348. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv' on page 52 undefined on input line 6348. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv-avek' on page 52 undefined on input line 6348. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv-ave k' on page 52 undefined on input line 6348. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 52 un defined on input line 6350. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 52 undefine d on input line 6350. Underfull \hbox (badness 5064) in paragraph at lines 6345--6358 \T1/ptm/m/n/10 Martyna-Tuckerman-Tobias-Klein im-ple-men-ta-tion, only use-able with \T1/pcr/m/sl/10 integrator=md[]vv LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-compressibility' on page 52 undefined on input line 6374. LaTeX Warning: Reference `user-guide/mdp-options:mdp-compressibility' on page 5 2 undefined on input line 6374. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-p' on page 52 un defined on input line 6375. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-p' on page 52 undefine d on input line 6375. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 52 un defined on input line 6375. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 52 undefine d on input line 6375. [52] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 53 un defined on input line 6386. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 53 undefine d on input line 6386. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-compressibility' on page 53 undefined on input line 6386. LaTeX Warning: Reference `user-guide/mdp-options:mdp-compressibility' on page 5 3 undefined on input line 6386. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-p' on page 53 un defined on input line 6387. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-p' on page 53 undefine d on input line 6387. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-compressibility' on page 53 undefined on input line 6403. LaTeX Warning: Reference `user-guide/mdp-options:mdp-compressibility' on page 5 3 undefined on input line 6403. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-p' on page 53 un defined on input line 6403. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-p' on page 53 undefine d on input line 6403. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-p' on page 53 un defined on input line 6438. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-p' on page 53 undefine d on input line 6438. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-compressibility' on page 53 undefined on input line 6441. LaTeX Warning: Reference `user-guide/mdp-options:mdp-compressibility' on page 5 3 undefined on input line 6441. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 53 undefined on input line 6463. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 53 und efined on input line 6463. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 53 undefined on input line 6468. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 53 und efined on input line 6468. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pcoupltype' on page 53 undefined on input line 6500. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pcoupltype' on page 53 und efined on input line 6500. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pcoupltype' on page 53 undefined on input line 6515. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pcoupltype' on page 53 und efined on input line 6515. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:reference -manual-position-restraints' on page 53 undefined on input line 6537. LaTeX Warning: Reference `reference-manual/functions/restraints:reference-manua l-position-restraints' on page 53 undefined on input line 6537. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:reference -manual-position-restraints' on page 53 undefined on input line 6573. LaTeX Warning: Reference `reference-manual/functions/restraints:reference-manua l-position-restraints' on page 53 undefined on input line 6573. [53] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-annealing-npoints' o n page 54 undefined on input line 6680. LaTeX Warning: Reference `user-guide/mdp-options:mdp-annealing-npoints' on page 54 undefined on input line 6680. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-annealing-npoints' o n page 54 undefined on input line 6695. LaTeX Warning: Reference `user-guide/mdp-options:mdp-annealing-npoints' on page 54 undefined on input line 6695. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 54 un defined on input line 6713. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 54 undefine d on input line 6713. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 54 un defined on input line 6747. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 54 undefine d on input line 6747. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-gen-temp' on page 54 undefined on input line 6748. LaTeX Warning: Reference `user-guide/mdp-options:mdp-gen-temp' on page 54 undef ined on input line 6748. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-gen-seed' on page 54 undefined on input line 6749. LaTeX Warning: Reference `user-guide/mdp-options:mdp-gen-seed' on page 54 undef ined on input line 6749. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 54 undefined on input line 6750. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 54 undefined on input line 6750. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-gen-seed' on page 54 undefined on input line 6782. LaTeX Warning: Reference `user-guide/mdp-options:mdp-gen-seed' on page 54 undef ined on input line 6782. [54] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-order' on page 55 undefined on input line 6894. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-order' on page 55 un defined on input line 6894. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 undefined on input line 6898. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 und efined on input line 6898. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlog' on page 55 u ndefined on input line 6900. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlog' on page 55 undefin ed on input line 6900. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-warnangle' on page 55 undefined on input line 6901. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-warnangle' on page 5 5 undefined on input line 6901. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-shake-tol' on page 5 5 undefined on input line 6918. LaTeX Warning: Reference `user-guide/mdp-options:mdp-shake-tol' on page 55 unde fined on input line 6918. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-order' on page 55 undefined on input line 7004. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-order' on page 55 un defined on input line 7004. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-order' on page 55 undefined on input line 7006. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-order' on page 55 un defined on input line 7006. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 undefined on input line 7006. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 und efined on input line 7006. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 undefined on input line 7007. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-iter' on page 55 und efined on input line 7007. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lincs-order' on page 55 undefined on input line 7008. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lincs-order' on page 55 un defined on input line 7008. [55] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pbc' on page 56 unde fined on input line 7112. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pbc' on page 56 undefined on input line 7112. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wall-atomtype' on pa ge 56 undefined on input line 7117. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wall-atomtype' on page 56 undefined on input line 7117. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nwall' on page 56 un defined on input line 7118. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nwall' on page 56 undefine d on input line 7118. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-energygrp-table' on page 56 undefined on input line 7197. LaTeX Warning: Reference `user-guide/mdp-options:mdp-energygrp-table' on page 5 6 undefined on input line 7197. [56] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wall-type' on page 5 7 undefined on input line 7220. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wall-type' on page 57 unde fined on input line 7220. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nwall' on page 57 un defined on input line 7252. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nwall' on page 57 undefine d on input line 7252. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ewald-geometry' on p age 57 undefined on input line 7252. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ewald-geometry' on page 57 undefined on input line 7252. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-ncoords' on pag e 57 undefined on input line 7265. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-ncoords' on page 57 u ndefined on input line 7265. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 57 u ndefined on input line 7265. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 57 undefin ed on input line 7265. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 57 undefined on input line 7267. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 5 7 undefined on input line 7267. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 57 u ndefined on input line 7287. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 57 undefin ed on input line 7287. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-cylinder' on page 57 undefined on input line 7319. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -cylinder' on page 57 undefined on input line 7319. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-dim' on page 57 undefined on input line 7441. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-dim' on page 5 7 undefined on input line 7441. [57] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on page 58 undefined on input line 7494. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on pa ge 58 undefined on input line 7494. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on page 58 undefined on input line 7510. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on pa ge 58 undefined on input line 7510. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on page 58 undefined on input line 7674. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-group1-pbcatom' on pa ge 58 undefined on input line 7674. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 58 un defined on input line 7676. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 58 undefine d on input line 7676. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-geometry ' on page 58 undefined on input line 7679. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-geometry' on p age 58 undefined on input line 7679. [58] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7735. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7735. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-rate' on page 59 undefined on input line 7736. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-rate' on page 59 undefined on input line 7736. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7749. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7749. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7763. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 59 undefined on input line 7763. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ty pe-external-potential' on page 59 undefined on input line 7795. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-type-ext ernal-potential' on page 59 undefined on input line 7795. Underfull \hbox (badness 10000) in paragraph at lines 7792--7796 \T1/ptm/m/n/10 The name of the ex-ter-nal mod-ule that pro-vides the po-ten-tia l for the case where LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-dim' on page 59 undefined on input line 7816. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-dim' on page 5 9 undefined on input line 7816. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 59 undefined on input line 7829. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 5 9 undefined on input line 7829. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-direction' on page 59 undefined on input line 7842. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -direction' on page 59 undefined on input line 7842. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-direction' on page 59 undefined on input line 7861. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -direction' on page 59 undefined on input line 7861. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-groups' on page 59 undefined on input line 7864. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-groups' on pag e 59 undefined on input line 7864. [59] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 60 undefined on input line 7884. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 6 0 undefined on input line 7884. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-groups' on page 60 undefined on input line 7885. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-groups' on pag e 60 undefined on input line 7885. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 60 undefined on input line 7887. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 6 0 undefined on input line 7887. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-cylinder-r' on page 60 undefined on input line 7888. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-cylinder-r' on page 6 0 undefined on input line 7888. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-cylinder-r' on page 60 undefined on input line 7890. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-cylinder-r' on page 6 0 undefined on input line 7890. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-angle' on page 60 undefined on input line 7927. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -angle' on page 60 undefined on input line 7927. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 60 undefined on input line 7927. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 6 0 undefined on input line 7927. Underfull \hbox (badness 7186) in paragraph at lines 7925--7929 \T1/ptm/m/n/10 As \T1/pcr/m/sl/10 pull[]coord1[]geometry=angle \T1/ptm/m/n/10 ( page []) but the sec-ond vec-tor is given by LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-expressi on' on page 60 undefined on input line 7959. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-expression' on page 60 undefined on input line 7959. Underfull \hbox (badness 10000) in paragraph at lines 7957--7963 \T1/ptm/m/n/10 Trans-forms other pull co-or-di-nates us-ing a math-e-mat-i-cal ex-pres-sion de-fined by LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-transformation' on page 60 undefined on input line 7984. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -transformation' on page 60 undefined on input line 7984. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-transformation' on page 60 undefined on input line 8002. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -transformation' on page 60 undefined on input line 8002. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-origin' on page 60 undefined on input line 8018. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-origin' on pag e 60 undefined on input line 8018. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-print-component s' on page 60 undefined on input line 8037. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-print-components' on page 60 undefined on input line 8037. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-st art-yes' on page 60 undefined on input line 8037. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-start-ye s' on page 60 undefined on input line 8037. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-geometry ' on page 60 undefined on input line 8038. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-geometry' on p age 60 undefined on input line 8038. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ge ometry-distance' on page 60 undefined on input line 8038. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-geometry -distance' on page 60 undefined on input line 8038. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 60 undefined on input line 8042. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-vec' on page 6 0 undefined on input line 8042. [60] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 61 un defined on input line 8071. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 61 undefine d on input line 8071. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8091. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8091. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8105. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8105. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8158. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-init' on page 61 undefined on input line 8158. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-rate' on page 61 undefined on input line 8158. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-rate' on page 61 undefined on input line 8158. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-k' on pa ge 61 undefined on input line 8173. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-k' on page 61 undefined on input line 8173. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-free-energy' on page 61 undefined on input line 8174. LaTeX Warning: Reference `user-guide/mdp-options:mdp-free-energy' on page 61 un defined on input line 8174. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-k' on pa ge 61 undefined on input line 8175. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-k' on page 61 undefined on input line 8175. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-kB' on p age 61 undefined on input line 8175. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-kB' on page 61 undefined on input line 8175. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 61 u ndefined on input line 8214. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 61 undefin ed on input line 8214. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-nstout' on page 61 undefined on input line 8214. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-nstout' on page 61 und efined on input line 8214. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-free-energy' on page 61 undefined on input line 8217. LaTeX Warning: Reference `user-guide/mdp-options:mdp-free-energy' on page 61 un defined on input line 8217. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pull-coord1-ty pe-external-potential' on page 61 undefined on input line 8218. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pull-coord1-type-ext ernal-potential' on page 61 undefined on input line 8218. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-potentia l-provider' on page 61 undefined on input line 8219. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-potential-prov ider' on page 61 undefined on input line 8219. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh-potential- umbrella' on page 61 undefined on input line 8245. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh-potential-umbrel la' on page 61 undefined on input line 8245. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-force-cons tant' on page 61 undefined on input line 8247. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-force-constant' on page 61 undefined on input line 8247. [61] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-force-cons tant' on page 62 undefined on input line 8263. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-force-constant' on page 62 undefined on input line 8263. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-nstsample' on pa ge 62 undefined on input line 8264. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-nstsample' on page 62 undefined on input line 8264. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 unde fined on input line 8292. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 undefined on input line 8292. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 unde fined on input line 8305. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 undefined on input line 8305. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 62 undefined on input line 8306. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 62 undefined on input line 8306. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 62 undefined on input line 8307. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 62 undefined on input line 8307. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 unde fined on input line 8309. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 62 undefined on input line 8309. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh-potential- umbrella' on page 62 undefined on input line 8329. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh-potential-umbrel la' on page 62 undefined on input line 8329. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstenergy' on page 6 2 undefined on input line 8344. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstenergy' on page 62 unde fined on input line 8344. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-nstsample' on pa ge 62 undefined on input line 8374. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-nstsample' on page 62 undefined on input line 8374. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-diffusion' on page 62 undefined on input line 8407. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-diffusion' on pa ge 62 undefined on input line 8407. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-error-init' on page 62 undefined on input line 8409. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-error-init' on page 6 2 undefined on input line 8409. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-error-init' on page 62 undefined on input line 8411. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-error-init' on page 6 2 undefined on input line 8411. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-user-data' on p age 62 undefined on input line 8413. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-user-data' on page 62 undefined on input line 8413. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-error-init' on page 62 undefined on input line 8414. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-error-init' on page 6 2 undefined on input line 8414. [62] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-nstsample' on pa ge 63 undefined on input line 8441. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-nstsample' on page 63 undefined on input line 8441. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 63 undefined on input line 8456. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 63 undefined on input line 8456. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-error-init' on page 63 undefined on input line 8457. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-error-init' on page 6 3 undefined on input line 8457. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-lo cal-boltzmann' on page 63 undefined on input line 8458. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-local-bo ltzmann' on page 63 undefined on input line 8458. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 63 undefined on input line 8475. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 63 undefined on input line 8475. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 63 undefined on input line 8509. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 63 undefined on input line 8509. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 63 undefined on input line 8512. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 63 undefined on input line 8512. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 63 undefined on input line 8538. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 6 3 undefined on input line 8538. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-end' on pa ge 63 undefined on input line 8538. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-end' on page 63 undefined on input line 8538. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-co nstant' on page 63 undefined on input line 8551. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-constant ' on page 63 undefined on input line 8551. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-cu toff' on page 63 undefined on input line 8552. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-cutoff' on page 63 undefined on input line 8552. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-target-beta-sca ling' on page 63 undefined on input line 8570. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-target-beta-scaling' on page 63 undefined on input line 8570. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-target-beta-sca ling' on page 63 undefined on input line 8585. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-target-beta-scaling' on page 63 undefined on input line 8585. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-li near' on page 63 undefined on input line 8588. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-linear' on page 63 undefined on input line 8588. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 63 undefined on input line 8589. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 63 undefined on input line 8589. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-bo ltzmann' on page 63 undefined on input line 8606. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-boltzman n' on page 63 undefined on input line 8606. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-lo cal-boltzmann' on page 63 undefined on input line 8606. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-local-bo ltzmann' on page 63 undefined on input line 8606. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-target-cu toff' on page 63 undefined on input line 8621. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-target-cutoff' on page 63 undefined on input line 8621. [63] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-nbias' on page 6 4 undefined on input line 8654. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-nbias' on page 64 unde fined on input line 8654. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 unde fined on input line 8655. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 undefined on input line 8655. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 unde fined on input line 8656. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 undefined on input line 8656. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-ndim' on page 6 4 undefined on input line 8658. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-ndim' on page 64 unde fined on input line 8658. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-ndim' on page 6 4 undefined on input line 8660. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-ndim' on page 64 unde fined on input line 8660. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-ndim' on page 6 4 undefined on input line 8661. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-ndim' on page 64 unde fined on input line 8661. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 64 undefine d on input line 8662. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 64 undefined on i nput line 8662. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 64 undefined on input line 8702. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 64 undefined on input line 8702. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh-share-mult isim-yes' on page 64 undefined on input line 8703. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh-share-multisim-y es' on page 64 undefined on input line 8703. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 unde fined on input line 8703. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 64 undefined on input line 8703. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-target' on page 64 undefined on input line 8748. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-target' on page 64 un defined on input line 8748. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-user-data' on p age 64 undefined on input line 8749. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-user-data' on page 64 undefined on input line 8749. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 64 undefined on input line 8749. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 64 undefined on input line 8749. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-free-energy' on page 64 undefined on input line 8820. LaTeX Warning: Reference `user-guide/mdp-options:mdp-free-energy' on page 64 un defined on input line 8820. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 64 undefined on input line 8822. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 64 un defined on input line 8822. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-vdw-lambdas' on page 64 undefined on input line 8822. LaTeX Warning: Reference `user-guide/mdp-options:mdp-vdw-lambdas' on page 64 un defined on input line 8822. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-coul-lambdas' on pag e 64 undefined on input line 8823. LaTeX Warning: Reference `user-guide/mdp-options:mdp-coul-lambdas' on page 64 u ndefined on input line 8823. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh-potential- umbrella' on page 64 undefined on input line 8825. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh-potential-umbrel la' on page 64 undefined on input line 8825. [64] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-pull-coord1-geometry ' on page 65 undefined on input line 8872. LaTeX Warning: Reference `user-guide/mdp-options:mdp-pull-coord1-geometry' on p age 65 undefined on input line 8872. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 65 undefined on input line 8873. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 6 5 undefined on input line 8873. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-end' on pa ge 65 undefined on input line 8873. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-end' on page 65 undefined on input line 8873. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 65 undefined on input line 8892. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-dim1-start' on page 6 5 undefined on input line 8892. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-awh1-growth-ex p-linear' on page 65 undefined on input line 8925. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-awh1-growth-exp-line ar' on page 65 undefined on input line 8925. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 65 undefined on input line 8929. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 65 undefined on input line 8929. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 65 u ndefined on input line 8942. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 65 undefin ed on input line 8942. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 65 u ndefined on input line 8962. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 65 undefin ed on input line 8962. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rot-type0' on page 6 5 undefined on input line 8976. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rot-type0' on page 65 unde fined on input line 8976. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rot-group0' on page 65 undefined on input line 8977. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rot-group0' on page 65 und efined on input line 8977. [65] [66] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-disre-tau' on page 6 7 undefined on input line 9305. LaTeX Warning: Reference `user-guide/mdp-options:mdp-disre-tau' on page 67 unde fined on input line 9305. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-dhdl-derivatives' on page 67 undefined on input line 9535. LaTeX Warning: Reference `user-guide/mdp-options:mdp-dhdl-derivatives' on page 67 undefined on input line 9535. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-calc-lambda-neighbor s' on page 67 undefined on input line 9537. LaTeX Warning: Reference `user-guide/mdp-options:mdp-calc-lambda-neighbors' on page 67 undefined on input line 9537. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 67 undefine d on input line 9539. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 67 undefined on i nput line 9539. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-alpha' on page 67 undefined on input line 9541. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-alpha' on page 67 undef ined on input line 9541. [67] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-delta-lambda' on pag e 68 undefined on input line 9578. LaTeX Warning: Reference `user-guide/mdp-options:mdp-delta-lambda' on page 68 u ndefined on input line 9578. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-state' o n page 68 undefined on input line 9579. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-state' on page 68 undefined on input line 9579. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda' on page 68 undefined on input line 9580. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda' on page 68 un defined on input line 9580. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-coul-lambdas' on pag e 68 undefined on input line 9611. LaTeX Warning: Reference `user-guide/mdp-options:mdp-coul-lambdas' on page 68 u ndefined on input line 9611. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-vdw-lambdas' on page 68 undefined on input line 9612. LaTeX Warning: Reference `user-guide/mdp-options:mdp-vdw-lambdas' on page 68 un defined on input line 9612. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-bonded-lambdas' on p age 68 undefined on input line 9612. LaTeX Warning: Reference `user-guide/mdp-options:mdp-bonded-lambdas' on page 68 undefined on input line 9612. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-restraint-lambdas' o n page 68 undefined on input line 9613. LaTeX Warning: Reference `user-guide/mdp-options:mdp-restraint-lambdas' on page 68 undefined on input line 9613. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-mass-lambdas' on pag e 68 undefined on input line 9613. LaTeX Warning: Reference `user-guide/mdp-options:mdp-mass-lambdas' on page 68 u ndefined on input line 9613. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-temperature-lambdas' on page 68 undefined on input line 9614. LaTeX Warning: Reference `user-guide/mdp-options:mdp-temperature-lambdas' on pa ge 68 undefined on input line 9614. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 undefined on input line 9614. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 un defined on input line 9614. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefined on input line 9631. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefi ned on input line 9631. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 68 undefine d on input line 9635. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 68 undefined on i nput line 9635. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 undefined on input line 9635. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 un defined on input line 9635. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 undefined on input line 9637. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 68 un defined on input line 9637. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefined on input line 9652. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefi ned on input line 9652. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefined on input line 9673. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefi ned on input line 9673. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefined on input line 9693. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefi ned on input line 9693. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefined on input line 9711. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 68 undefi ned on input line 9711. [68] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 69 undefined on input line 9730. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 69 undefi ned on input line 9730. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 69 undefined on input line 9748. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 69 undefi ned on input line 9748. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-state' o n page 69 undefined on input line 9768. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-state' on page 69 undefined on input line 9768. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-state' o n page 69 undefined on input line 9771. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-state' on page 69 undefined on input line 9771. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-state' o n page 69 undefined on input line 9772. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-state' on page 69 undefined on input line 9772. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 69 undefine d on input line 9775. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 69 undefined on i nput line 9775. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9829. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9829. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9832. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9832. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9847. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9847. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-alpha' on page 69 undefined on input line 9867. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-alpha' on page 69 undef ined on input line 9867. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9868. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9868. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9883. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9883. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9897. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9897. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-sigma' on page 69 undefined on input line 9899. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-sigma' on page 69 undef ined on input line 9899. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-be utler' on page 69 undefined on input line 9900. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-beutler' on page 69 undefined on input line 9900. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 69 undefined on input line 9914. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 69 undefined on input line 9914. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 69 undefined on input line 9919. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 69 undefined on input line 9919. [69] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 70 undefined on input line 9933. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 70 undefined on input line 9933. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 70 undefined on input line 9937. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 70 undefined on input line 9937. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 70 undefined on input line 9951. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 70 undefined on input line 9951. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-sc-function-ga psys' on page 70 undefined on input line 9953. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-sc-function-gapsys' on page 70 undefined on input line 9953. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-free-energy' on page 70 undefined on input line 9970. LaTeX Warning: Reference `user-guide/mdp-options:mdp-free-energy' on page 70 un defined on input line 9970. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-couple-lambda0' on p age 70 undefined on input line 9973. LaTeX Warning: Reference `user-guide/mdp-options:mdp-couple-lambda0' on page 70 undefined on input line 9973. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-couple-lambda1' on p age 70 undefined on input line 9974. LaTeX Warning: Reference `user-guide/mdp-options:mdp-couple-lambda1' on page 70 undefined on input line 9974. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-couple-lambda0' on p age 70 undefined on input line 10054. LaTeX Warning: Reference `user-guide/mdp-options:mdp-couple-lambda0' on page 70 undefined on input line 10054. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-couple-moltype' on p age 70 undefined on input line 10075. LaTeX Warning: Reference `user-guide/mdp-options:mdp-couple-moltype' on page 70 undefined on input line 10075. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcalcenergy' on pa ge 70 undefined on input line 10115. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcalcenergy' on page 70 undefined on input line 10115. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 70 undefined on input line 10132. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 70 undefi ned on input line 10132. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 70 undefine d on input line 10134. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 70 undefined on i nput line 10134. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-calc-lambda-neighbor s' on page 70 undefined on input line 10135. LaTeX Warning: Reference `user-guide/mdp-options:mdp-calc-lambda-neighbors' on page 70 undefined on input line 10135. [70] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-calc-lambda-neighbor s' on page 71 undefined on input line 10182. LaTeX Warning: Reference `user-guide/mdp-options:mdp-calc-lambda-neighbors' on page 71 undefined on input line 10182. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-dhdl-derivatives' on page 71 undefined on input line 10182. LaTeX Warning: Reference `user-guide/mdp-options:mdp-dhdl-derivatives' on page 71 undefined on input line 10182. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 71 undefine d on input line 10184. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 71 undefined on i nput line 10184. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstenergy' on page 7 1 undefined on input line 10198. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstenergy' on page 71 unde fined on input line 10198. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 71 un defined on input line 10199. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 71 undefine d on input line 10199. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 71 undefine d on input line 10200. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 71 undefined on i nput line 10200. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-calc-lambda-neighbor s' on page 71 undefined on input line 10218. LaTeX Warning: Reference `user-guide/mdp-options:mdp-calc-lambda-neighbors' on page 71 undefined on input line 10218. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstenergy' on page 7 1 undefined on input line 10222. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstenergy' on page 71 unde fined on input line 10222. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-dh-hist-size' on pag e 71 undefined on input line 10239. LaTeX Warning: Reference `user-guide/mdp-options:mdp-dh-hist-size' on page 71 u ndefined on input line 10239. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcalcenergy' on pa ge 71 undefined on input line 10259. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcalcenergy' on page 71 undefined on input line 10259. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstdhdl' on page 71 undefined on input line 10260. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstdhdl' on page 71 undefi ned on input line 10260. [71] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-seed' on page 72 undefined on input line 10445. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-seed' on page 72 undef ined on input line 10445. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-ref-t' on page 72 un defined on input line 10460. LaTeX Warning: Reference `user-guide/mdp-options:mdp-ref-t' on page 72 undefine d on input line 10460. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wl-scale' on page 72 undefined on input line 10476. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wl-scale' on page 72 undef ined on input line 10476. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wl-ratio' on page 72 undefined on input line 10478. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wl-ratio' on page 72 undef ined on input line 10478. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wl-scale' on page 72 undefined on input line 10496. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wl-scale' on page 72 undef ined on input line 10496. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wl-oneovert' on page 72 undefined on input line 10531. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wl-oneovert' on page 72 un defined on input line 10531. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-wl-ratio' on page 72 undefined on input line 10536. LaTeX Warning: Reference `user-guide/mdp-options:mdp-wl-ratio' on page 72 undef ined on input line 10536. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-weights-equil' o n page 72 undefined on input line 10538. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-weights-equil' on page 72 undefined on input line 10538. [72] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-gibbsdelta' on p age 73 undefined on input line 10572. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-gibbsdelta' on page 73 undefined on input line 10572. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-gibbsdelta' on p age 73 undefined on input line 10573. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-gibbsdelta' on page 73 undefined on input line 10573. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-forced-nstart' o n page 73 undefined on input line 10592. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-forced-nstart' on page 73 undefined on input line 10592. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-forced-nstart' o n page 73 undefined on input line 10593. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-forced-nstart' on page 73 undefined on input line 10593. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-stats' on page 7 3 undefined on input line 10644. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-stats' on page 73 unde fined on input line 10644. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-mininum-var-min' on page 73 undefined on input line 10646. LaTeX Warning: Reference `user-guide/mdp-options:mdp-mininum-var-min' on page 7 3 undefined on input line 10646. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 undefined on input line 10663. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 un defined on input line 10663. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 undefined on input line 10687. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 un defined on input line 10687. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-lmc-weights-equil' o n page 73 undefined on input line 10705. LaTeX Warning: Reference `user-guide/mdp-options:mdp-lmc-weights-equil' on page 73 undefined on input line 10705. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 undefined on input line 10718. LaTeX Warning: Reference `user-guide/mdp-options:mdp-fep-lambdas' on page 73 un defined on input line 10718. [73] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-temperature-lambdas' on page 74 undefined on input line 10888. LaTeX Warning: Reference `user-guide/mdp-options:mdp-temperature-lambdas' on pa ge 74 undefined on input line 10888. Underfull \hbox (badness 10000) in paragraph at lines 10885--10890 \T1/ptm/m/n/10 Con-trols the way that the tem-per-a-tures at in-ter-me-di-ate l amb-das are cal-cu-lated from the LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-temperature-lambdas' on page 74 undefined on input line 10900. LaTeX Warning: Reference `user-guide/mdp-options:mdp-temperature-lambdas' on pa ge 74 undefined on input line 10900. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10900. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10900. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-high' on pa ge 74 undefined on input line 10901. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-high' on page 74 undefined on input line 10901. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10917. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10917. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-high' on pa ge 74 undefined on input line 10917. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-high' on page 74 undefined on input line 10917. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10918. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10918. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-high' on pa ge 74 undefined on input line 10918. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-high' on page 74 undefined on input line 10918. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10919. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10919. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10936. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10936. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-high' on pa ge 74 undefined on input line 10936. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-high' on page 74 undefined on input line 10936. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10937. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10937. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-high' on pa ge 74 undefined on input line 10937. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-high' on page 74 undefined on input line 10937. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sim-temp-low' on pag e 74 undefined on input line 10938. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sim-temp-low' on page 74 u ndefined on input line 10938. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-temperature-lambdas' on page 74 undefined on input line 10938. LaTeX Warning: Reference `user-guide/mdp-options:mdp-temperature-lambdas' on pa ge 74 undefined on input line 10938. [74] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-accelerate' on page 75 undefined on input line 10960. LaTeX Warning: Reference `user-guide/mdp-options:mdp-accelerate' on page 75 und efined on input line 10960. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-acc-grps' on page 75 undefined on input line 10977. LaTeX Warning: Reference `user-guide/mdp-options:mdp-acc-grps' on page 75 undef ined on input line 10977. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-freezedim' on page 7 5 undefined on input line 10994. LaTeX Warning: Reference `user-guide/mdp-options:mdp-freezedim' on page 75 unde fined on input line 10994. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-freezegrps' on page 75 undefined on input line 11011. LaTeX Warning: Reference `user-guide/mdp-options:mdp-freezegrps' on page 75 und efined on input line 11011. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-cos-acceleration' on page 75 undefined on input line 11031. LaTeX Warning: Reference `user-guide/mdp-options:mdp-cos-acceleration' on page 75 undefined on input line 11031. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-deform' on page 75 u ndefined on input line 11048. LaTeX Warning: Reference `user-guide/mdp-options:mdp-deform' on page 75 undefin ed on input line 11048. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-deform-init-flow' on page 75 undefined on input line 11065. LaTeX Warning: Reference `user-guide/mdp-options:mdp-deform-init-flow' on page 75 undefined on input line 11065. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 75 unde fined on input line 11067. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 75 undefined on input line 11067. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-deform' on page 75 u ndefined on input line 11103. LaTeX Warning: Reference `user-guide/mdp-options:mdp-deform' on page 75 undefin ed on input line 11103. [75] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-electric-field-x' on page 76 undefined on input line 11153. LaTeX Warning: Reference `user-guide/mdp-options:mdp-electric-field-x' on page 76 undefined on input line 11153. LaTeX Warning: Hyper reference `reference-manual/special/electric-fields:electr ic-fields' on page 76 undefined on input line 11168. LaTeX Warning: Reference `reference-manual/special/electric-fields:electric-fie lds' on page 76 undefined on input line 11168. LaTeX Warning: Hyper reference `reference-manual/references:refcaleman2008a' on page 76 undefined on input line 11168. LaTeX Warning: Reference `reference-manual/references:refcaleman2008a' on page 76 undefined on input line 11168. [76] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-split-group1' on pag e 77 undefined on input line 11350. LaTeX Warning: Reference `user-guide/mdp-options:mdp-split-group1' on page 77 u ndefined on input line 11350. [77] Overfull \hbox (39.0321pt too wide) in paragraph at lines 11741--11741 []\T1/pcr/b/n/10 density[]guided[]simulation[]gaussian[]transform[]spreading[]r ange[]in[]multiples[]of[]width| LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 78 unde fined on input line 11759. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 78 undefined on input line 11759. [78] LaTeX Warning: Hyper reference `reference-manual/special/qmmm:qmmm' on page 79 undefined on input line 11877. LaTeX Warning: Reference `reference-manual/special/qmmm:qmmm' on page 79 undefi ned on input line 11877. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 79 un defined on input line 11949. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 79 undefine d on input line 11949. LaTeX Warning: Hyper reference `reference-manual/special/qmmm:qmmm' on page 79 undefined on input line 11950. LaTeX Warning: Reference `reference-manual/special/qmmm:qmmm' on page 79 undefi ned on input line 11950. [79] LaTeX Warning: Hyper reference `reference-manual/references:reffiorin13' on pag e 80 undefined on input line 12015. LaTeX Warning: Reference `reference-manual/references:reffiorin13' on page 80 u ndefined on input line 12015. LaTeX Warning: Hyper reference `reference-manual/special/colvars:colvars' on pa ge 80 undefined on input line 12018. LaTeX Warning: Reference `reference-manual/special/colvars:colvars' on page 80 undefined on input line 12018. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 80 un defined on input line 12047. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 80 undefine d on input line 12047. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 80 u ndefined on input line 12186. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 80 undefin ed on input line 12186. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 80 u ndefined on input line 12186. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 80 undefin ed on input line 12186. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 80 un defined on input line 12187. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 80 undefine d on input line 12187. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 80 unde fined on input line 12187. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 80 undefined on input line 12187. [80] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12222. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12222. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 81 u ndefined on input line 12232. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 81 undefin ed on input line 12232. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 81 undefined on input line 12236. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 8 1 undefined on input line 12236. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 81 undefined on input line 12237. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 81 undefi ned on input line 12237. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 81 undefined on input line 12242. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 81 undefi ned on input line 12242. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12243. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12243. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12261. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12261. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12275. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12275. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12278. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12278. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12283. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12283. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12285. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12285. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 unde fined on input line 12287. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 81 undefined on input line 12287. LaTeX Warning: Hyper reference `install-guide/index:mpi-support' on page 81 und efined on input line 12303. LaTeX Warning: Reference `install-guide/index:mpi-support' on page 81 undefined on input line 12303. [81] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 82 u ndefined on input line 12397. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 82 undefin ed on input line 12397. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsteps' on page 82 u ndefined on input line 12397. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsteps' on page 82 undefin ed on input line 12397. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 82 u ndefined on input line 12398. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 82 undefin ed on input line 12398. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 82 unde fined on input line 12417. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 82 undefined on input line 12417. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 82 unde fined on input line 12420. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 82 undefined on input line 12420. [82] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 83 unde fined on input line 12485. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 83 undefined on input line 12485. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 83 unde fined on input line 12488. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 83 undefined on input line 12488. [83] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 84 unde fined on input line 12557. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 84 undefined on input line 12557. LaTeX Warning: Hyper reference `reference-manual/index:gmx-reference-manual-rst ' on page 84 undefined on input line 12559. LaTeX Warning: Reference `reference-manual/index:gmx-reference-manual-rst' on p age 84 undefined on input line 12559. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 84 unde fined on input line 12576. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 84 undefined on input line 12576. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:controlling-the-do main-decomposition-algorithm' on page 84 undefined on input line 12578. LaTeX Warning: Reference `user-guide/mdrun-performance:controlling-the-domain-d ecomposition-algorithm' on page 84 undefined on input line 12578. [84] LaTeX Warning: Hyper reference `install-guide/index:gmx-simd-support' on page 8 5 undefined on input line 12611. LaTeX Warning: Reference `install-guide/index:gmx-simd-support' on page 85 unde fined on input line 12611. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12635. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12635. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12643. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12643. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12657. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12657. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12658. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12658. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12665. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12665. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12682. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12682. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12685. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12685. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12689. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12689. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 unde fined on input line 12693. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 85 undefined on input line 12693. [85] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 unde fined on input line 12697. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 undefined on input line 12697. LaTeX Warning: Hyper reference `install-guide/index:gmx-gpu-support' on page 86 undefined on input line 12717. LaTeX Warning: Reference `install-guide/index:gmx-gpu-support' on page 86 undef ined on input line 12717. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 unde fined on input line 12721. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 undefined on input line 12721. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 unde fined on input line 12734. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 undefined on input line 12734. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 86 undefined on input line 12739. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 86 undef ined on input line 12739. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 86 u ndefined on input line 12739. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 86 undefin ed on input line 12739. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-domain-decomp' on page 86 undefined on input line 12758. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-domain-decomp' on pa ge 86 undefined on input line 12758. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 unde fined on input line 12760. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 undefined on input line 12760. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 unde fined on input line 12781. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 86 undefined on input line 12781. [86] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 unde fined on input line 12787. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 undefined on input line 12787. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 unde fined on input line 12800. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 undefined on input line 12800. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 unde fined on input line 12808. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 undefined on input line 12808. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 8 7 undefined on input line 12866. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 87 unde fined on input line 12866. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 unde fined on input line 12869. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 87 undefined on input line 12869. [87] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12879. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12879. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:term-node' on page 88 undefined on input line 12880. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12888. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12888. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12892. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12892. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12918. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12918. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12941. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12941. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12942. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12942. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12943. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12943. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12950. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12950. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12951. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12951. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12952. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12952. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12957. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12957. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12958. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12958. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12959. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12959. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 unde fined on input line 12961. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 88 undefined on input line 12961. [88] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 unde fined on input line 13026. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 undefined on input line 13026. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 unde fined on input line 13029. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 undefined on input line 13029. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 unde fined on input line 13032. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 undefined on input line 13032. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 unde fined on input line 13047. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 undefined on input line 13047. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:assigning-tasks-to -gpus' on page 89 undefined on input line 13050. LaTeX Warning: Reference `user-guide/mdrun-performance:assigning-tasks-to-gpus' on page 89 undefined on input line 13050. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 unde fined on input line 13068. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 89 undefined on input line 13068. [89] LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-tasks' on page 90 undefined on input line 13091. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-tasks' on page 9 0 undefined on input line 13091. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13113. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13113. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13113. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13113. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13124. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13124. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13133. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13133. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13147. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13147. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13160. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13160. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 unde fined on input line 13170. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 90 undefined on input line 13170. [90] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13182. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13182. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13205. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13205. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13216. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13216. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13223. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13223. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13234. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13234. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13238. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13238. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13245. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13245. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13247. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13247. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 unde fined on input line 13270. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 91 undefined on input line 13270. [91] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13289. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13289. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-general' on page 92 undefined on input line 13292. LaTeX Warning: Reference `user-guide/mdp-options:mdp-general' on page 92 undefi ned on input line 13292. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstcalcenergy' on pa ge 92 undefined on input line 13294. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstcalcenergy' on page 92 undefined on input line 13294. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 92 undefined on input line 13295. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 92 und efined on input line 13295. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 92 undefined on input line 13295. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 92 und efined on input line 13295. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:term-node' on page 92 undefined on input line 13299. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 9 2 undefined on input line 13310. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 92 unde fined on input line 13310. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 92 u ndefined on input line 13312. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 92 undefin ed on input line 13312. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13321. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13321. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13330. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13330. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13351. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13351. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13362. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13362. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13372. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13372. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13383. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13383. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13393. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13393. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 unde fined on input line 13398. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 92 undefined on input line 13398. [92] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 unde fined on input line 13405. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 undefined on input line 13405. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 unde fined on input line 13461. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 undefined on input line 13461. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 unde fined on input line 13463. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 undefined on input line 13463. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 unde fined on input line 13469. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 93 undefined on input line 13469. [93] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 94 unde fined on input line 13640. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 94 undefined on input line 13640. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 94 unde fined on input line 13648. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 94 undefined on input line 13648. [94] LaTeX Warning: Hyper reference `dev-manual/build-system::doc' on page 95 undefi ned on input line 13745. LaTeX Warning: Reference `dev-manual/build-system::doc' on page 95 undefined on input line 13745. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-pp' on pag e 95 undefined on input line 13755. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-pp' on page 95 u ndefined on input line 13755. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-pme' on pa ge 95 undefined on input line 13755. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-pme' on page 95 undefined on input line 13755. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-bonded' on page 95 undefined on input line 13756. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-bonded' on page 95 undefined on input line 13756. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-update' on page 95 undefined on input line 13757. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-update' on page 95 undefined on input line 13757. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-domain-decomp' on page 95 undefined on input line 13766. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-domain-decomp' on pa ge 95 undefined on input line 13766. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-pp' on pag e 95 undefined on input line 13778. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-pp' on page 95 u ndefined on input line 13778. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-pme' on pa ge 95 undefined on input line 13779. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-pme' on page 95 undefined on input line 13779. [95] LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-pme-gpu-limita tions' on page 96 undefined on input line 13795. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-pme-gpu-limitations' on page 96 undefined on input line 13795. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-gpu-update' on page 96 undefined on input line 13798. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-gpu-update' on page 96 undefined on input line 13798. LaTeX Warning: Hyper reference `install-guide/index:cufftmp-installation' on pa ge 96 undefined on input line 13834. LaTeX Warning: Reference `install-guide/index:cufftmp-installation' on page 96 undefined on input line 13834. LaTeX Warning: Hyper reference `install-guide/index:heffte-installation' on pag e 96 undefined on input line 13835. LaTeX Warning: Reference `install-guide/index:heffte-installation' on page 96 u ndefined on input line 13835. [96] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 97 unde fined on input line 13910. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 97 undefined on input line 13910. [97] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 unde fined on input line 14028. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 undefined on input line 14028. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 unde fined on input line 14069. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 undefined on input line 14069. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 unde fined on input line 14103. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 undefined on input line 14103. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 unde fined on input line 14109. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 98 undefined on input line 14109. [98] LaTeX Warning: Hyper reference `user-guide/mdrun-performance:opencl-known-limit ations' on page 99 undefined on input line 14150. LaTeX Warning: Reference `user-guide/mdrun-performance:opencl-known-limitations ' on page 99 undefined on input line 14150. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 99 unde fined on input line 14161. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 99 undefined on input line 14161. LaTeX Warning: Hyper reference `user-guide/environment-variables:opencl-managem ent' on page 99 undefined on input line 14171. LaTeX Warning: Reference `user-guide/environment-variables:opencl-management' o n page 99 undefined on input line 14171. [99] LaTeX Warning: Hyper reference `install-guide/index:sycl-gpu-acceleration' on p age 100 undefined on input line 14212. LaTeX Warning: Reference `install-guide/index:sycl-gpu-acceleration' on page 10 0 undefined on input line 14212. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 100 und efined on input line 14224. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 100 undefined on input line 14224. LaTeX Warning: Hyper reference `install-guide/index:amd-hip' on page 100 undefi ned on input line 14239. LaTeX Warning: Reference `install-guide/index:amd-hip' on page 100 undefined on input line 14239. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 100 und efined on input line 14307. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 100 undefined on input line 14307. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:intra-core-paralle lization' on page 100 undefined on input line 14310. LaTeX Warning: Reference `user-guide/mdrun-performance:intra-core-parallelizati on' on page 100 undefined on input line 14310. [100] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-constraints-h- bonds' on page 101 undefined on input line 14330. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-constraints-h-bonds' on page 101 undefined on input line 14330. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-constraints-al l-bonds' on page 101 undefined on input line 14331. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-constraints-all-bond s' on page 101 undefined on input line 14331. Underfull \hbox (badness 6927) in paragraph at lines 14329--14333 []\T1/ptm/m/n/10 When us-ing a time-step of <=2.5 fs, use \T1/pcr/m/sl/10 const raints=h[]bonds \T1/ptm/m/n/10 (page []) (and not LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 1 01 undefined on input line 14362. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 101 und efined on input line 14362. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 101 und efined on input line 14410. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 101 undefined on input line 14410. [101] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14479. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14479. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 102 undefined on input line 14479. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 102 undef ined on input line 14479. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14506. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14506. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14507. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14507. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14507. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14507. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14510. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14510. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 102 undefined on input line 14510. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 102 undefi ned on input line 14510. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14510. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14510. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14515. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14515. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 102 undefined on input line 14516. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 102 undefi ned on input line 14516. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 102 undefined on input line 14516. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 102 u ndefined on input line 14516. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14518. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14518. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14521. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14521. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14522. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14522. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 102 undefined on input line 14522. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 102 u ndefined on input line 14522. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14524. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14524. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14525. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14525. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 102 undefined on input line 14528. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 102 undefi ned on input line 14528. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undefined on input line 14528. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 102 undef ined on input line 14528. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14529. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14529. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 102 und efined on input line 14530. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 102 undefined on input line 14530. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 102 undefined on input line 14530. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 102 undefi ned on input line 14530. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 102 undefined on input line 14539. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 102 undefi ned on input line 14539. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 102 undefined on input line 14547. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 102 undefi ned on input line 14547. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 102 undefined on input line 14548. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 102 undefi ned on input line 14548. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 102 undefined on input line 14548. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 102 undefi ned on input line 14548. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 102 undefined on input line 14552. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 102 u ndefined on input line 14552. [102] LaTeX Warning: Hyper reference `how-to/topology:gmx-add-residue' on page 103 un defined on input line 14563. LaTeX Warning: Reference `how-to/topology:gmx-add-residue' on page 103 undefine d on input line 14563. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 103 undefined on input line 14569. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 103 undefi ned on input line 14569. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14569. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14569. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14570. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14570. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 103 undefined on input line 14571. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 103 undefi ned on input line 14571. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 103 undefined on input line 14578. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 103 undefined on input line 14578. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14578. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14578. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14589. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14589. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 103 undefined on input line 14590. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 103 undefi ned on input line 14590. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 103 undefined on input line 14595. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 103 undefi ned on input line 14595. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 103 undefined on input line 14597. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 103 undefi ned on input line 14597. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14598. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14598. LaTeX Warning: Hyper reference `user-guide/force-fields:gmx-amber-ff' on page 1 03 undefined on input line 14605. LaTeX Warning: Reference `user-guide/force-fields:gmx-amber-ff' on page 103 und efined on input line 14605. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 103 undefined on input line 14607. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 103 undefi ned on input line 14607. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14613. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14613. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 103 undefined on input line 14614. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 103 undefi ned on input line 14614. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 103 undefined on input line 14624. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 103 undefi ned on input line 14624. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14632. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14632. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 103 undefined on input line 14633. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 103 undefi ned on input line 14633. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 103 undefined on input line 14635. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 103 undefined on input line 14635. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 103 undefined on input line 14637. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 103 u ndefined on input line 14637. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 103 undefined on input line 14639. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 103 u ndefined on input line 14639. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undefined on input line 14646. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 103 undef ined on input line 14646. LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 103 undefined on input line 14649. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 103 undefined on input line 14649. [103] LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14659. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14659. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14660. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14660. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14661. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14661. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 104 undefined on input line 14661. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 104 undefi ned on input line 14661. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14682. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14682. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14683. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14683. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14684. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14684. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 104 undefined on input line 14685. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 104 undefi ned on input line 14685. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-topo-include' on page 104 undefined on input line 14694. LaTeX Warning: Reference `user-guide/getting-started:gmx-topo-include' on page 104 undefined on input line 14694. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14699. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14699. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14699. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14699. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14701. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14701. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14701. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14701. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 104 undefined on input line 14702. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 104 undefi ned on input line 14702. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 104 undefined on input line 14709. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 104 u ndefined on input line 14709. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 104 undefined on input line 14717. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 104 undefi ned on input line 14717. [104] LaTeX Warning: Hyper reference `onlinehelp/gmx-genrestr:gmx-genrestr' on page 1 05 undefined on input line 14759. LaTeX Warning: Reference `onlinehelp/gmx-genrestr:gmx-genrestr' on page 105 und efined on input line 14759. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 105 undefined on input line 14769. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 105 undefi ned on input line 14769. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 105 undefined on input line 14770. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 105 undef ined on input line 14770. LaTeX Warning: Hyper reference `user-guide/floating-point:gmx-floating-point' o n page 105 undefined on input line 14778. LaTeX Warning: Reference `user-guide/floating-point:gmx-floating-point' on page 105 undefined on input line 14778. LaTeX Warning: Hyper reference `reference-manual/references:refgroenhofewaldart efact' on page 105 undefined on input line 14784. LaTeX Warning: Reference `reference-manual/references:refgroenhofewaldartefact' on page 105 undefined on input line 14784. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 105 undefined on input line 14791. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 105 undefi ned on input line 14791. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-topo-include' on page 105 undefined on input line 14792. LaTeX Warning: Reference `user-guide/getting-started:gmx-topo-include' on page 105 undefined on input line 14792. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 105 undefined on input line 14799. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 105 undefi ned on input line 14799. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 105 undefined on input line 14799. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 105 undefi ned on input line 14799. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 105 undefined on input line 14801. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 105 undefined on input line 14801. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 105 undefined on input line 14801. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 105 undefi ned on input line 14801. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 105 undefined on input line 14801. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 105 undefi ned on input line 14801. [105] LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14822. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14822. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14823. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14823. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-topo-include' on page 106 undefined on input line 14824. LaTeX Warning: Reference `user-guide/getting-started:gmx-topo-include' on page 106 undefined on input line 14824. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 106 undefined on input line 14824. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 106 undefi ned on input line 14824. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14825. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14825. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-thermostats' on page 106 undefined on input line 14834. LaTeX Warning: Reference `user-guide/terminology:gmx-thermostats' on page 106 u ndefined on input line 14834. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 106 undefined on input line 14854. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 106 u ndefined on input line 14854. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14873. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14873. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 106 undefined on input line 14875. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 106 undefi ned on input line 14875. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-topo-include' on page 106 undefined on input line 14878. LaTeX Warning: Reference `user-guide/getting-started:gmx-topo-include' on page 106 undefined on input line 14878. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14884. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14884. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 106 undefined on input line 14885. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 106 undefined on input line 14885. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 106 u ndefined on input line 14885. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 106 undefin ed on input line 14885. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 106 undefined on input line 14886. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 106 undefi ned on input line 14886. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 106 undefined on input line 14887. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 106 undefined on input line 14887. LaTeX Warning: Hyper reference `reference-manual/file-formats:gmx-structure-fil es' on page 106 undefined on input line 14893. LaTeX Warning: Reference `reference-manual/file-formats:gmx-structure-files' on page 106 undefined on input line 14893. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 106 u ndefined on input line 14894. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 106 undefin ed on input line 14894. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 106 undefined on input line 14897. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 106 undefi ned on input line 14897. [106] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 107 undefined on input line 14903. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 107 undefi ned on input line 14903. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 107 undefined on input line 14904. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 107 undefi ned on input line 14904. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 107 u ndefined on input line 14905. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 107 undefin ed on input line 14905. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 107 und efined on input line 14953. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 107 undefined on input line 14953. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 107 undefined on input line 14954. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 107 undefi ned on input line 14954. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 107 undefined on input line 14955. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 107 undefi ned on input line 14955. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 107 undefined on input line 14956. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 107 undefi ned on input line 14956. LaTeX Warning: Hyper reference `user-guide/terminology:system-diagnosis' on pag e 107 undefined on input line 14960. LaTeX Warning: Reference `user-guide/terminology:system-diagnosis' on page 107 undefined on input line 14960. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 107 undefined on input line 14969. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 107 undefi ned on input line 14969. [107] LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 108 undefined on input line 14980. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 108 undefi ned on input line 14980. LaTeX Warning: Hyper reference `user-guide/mdrun-performance:gmx-performance' o n page 108 undefined on input line 14991. LaTeX Warning: Reference `user-guide/mdrun-performance:gmx-performance' on page 108 undefined on input line 14991. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 108 undefined on input line 15004. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 108 undefi ned on input line 15004. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 108 und efined on input line 15008. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 108 undefined on input line 15008. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 108 undefined on input line 15027. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 108 undefi ned on input line 15027. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-tau-p' on page 108 u ndefined on input line 15037. LaTeX Warning: Reference `user-guide/mdp-options:mdp-tau-p' on page 108 undefin ed on input line 15037. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 108 undefined on input line 15050. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 108 undefi ned on input line 15050. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 108 und efined on input line 15057. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 108 undefined on input line 15057. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 108 undefined on input line 15057. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 108 undefi ned on input line 15057. LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 108 undefined on input line 15061. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 108 undefi ned on input line 15061. [108] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 und efined on input line 15079. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 undefined on input line 15079. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 109 u ndefined on input line 15084. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 109 undefin ed on input line 15084. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 und efined on input line 15085. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 undefined on input line 15085. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 109 undefined on input line 15086. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 109 undefi ned on input line 15086. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 und efined on input line 15090. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 109 undefined on input line 15090. [109] [110] [111] [112] [113] [114] [115] LaTeX Warning: Hyper reference `onlinehelp/gmx-covar::doc' on page 116 undefine d on input line 15766. LaTeX Warning: Reference `onlinehelp/gmx-covar::doc' on page 116 undefined on i nput line 15766. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig::doc' on page 116 undefine d on input line 15767. LaTeX Warning: Reference `onlinehelp/gmx-nmeig::doc' on page 116 undefined on i nput line 15767. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze::doc' on page 116 undefi ned on input line 15794. LaTeX Warning: Reference `onlinehelp/gmx-analyze::doc' on page 116 undefined on input line 15794. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 116 undefined on input line 15815. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 116 undefi ned on input line 15815. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 116 undefined on input line 15816. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 116 undefi ned on input line 15816. [116] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 117 undefined on input line 15868. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 117 undefi ned on input line 15868. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 117 undefined on input line 15868. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 117 undefi ned on input line 15868. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 117 undefined on input line 15868. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 117 undefi ned on input line 15868. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 117 undefined on input line 15872. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 117 undefi ned on input line 15872. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 117 undefined on input line 15872. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 117 undefi ned on input line 15872. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 117 undefined on input line 15872. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 117 undefi ned on input line 15872. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 117 undefined on input line 15876. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 117 undefi ned on input line 15876. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 117 undefined on input line 15880. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 117 undefi ned on input line 15880. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 117 undefined on input line 15880. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 117 undefi ned on input line 15880. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 117 undefined on input line 15880. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 117 undefi ned on input line 15880. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 117 undefined on input line 15880. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 117 undefi ned on input line 15880. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 117 undefined on input line 15917. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 117 undefi ned on input line 15917. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 117 undefined on input line 15917. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 117 undefi ned on input line 15917. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 117 undefined on input line 15917. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 117 undefi ned on input line 15917. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 117 undefined on input line 15921. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 117 undefi ned on input line 15921. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 117 undefi ned on input line 15925. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 117 undefined on input line 15925. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 117 undefi ned on input line 15925. [117] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 118 undefined on input line 15958. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 118 undefi ned on input line 15958. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 118 undefined on input line 15958. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 118 undefi ned on input line 15958. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 118 undefined on input line 15958. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 118 undefi ned on input line 15958. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 118 undefined on input line 15958. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 118 undefi ned on input line 15958. [118] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond::doc' on page 119 undefine d on input line 16129. LaTeX Warning: Reference `onlinehelp/gmx-hbond::doc' on page 119 undefined on i nput line 16129. [119] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 120 undefined on input line 16194. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 120 undefi ned on input line 16194. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 120 undefined on input line 16194. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 120 undefi ned on input line 16194. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 120 undefined on input line 16194. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 120 undefi ned on input line 16194. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 120 undefined on input line 16194. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 120 undefi ned on input line 16194. [120] LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond::doc' on page 121 undefine d on input line 16246. LaTeX Warning: Reference `onlinehelp/gmx-hbond::doc' on page 121 undefined on i nput line 16246. [121] LaTeX Warning: Hyper reference `onlinehelp/gmx-covar::doc' on page 122 undefine d on input line 16348. LaTeX Warning: Reference `onlinehelp/gmx-covar::doc' on page 122 undefined on i nput line 16348. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 122 undefined on input line 16364. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 122 undefi ned on input line 16364. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 122 undefined on input line 16422. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 122 undefi ned on input line 16422. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 122 undefined on input line 16422. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 122 undefi ned on input line 16422. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 122 undefined on input line 16422. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 122 undefi ned on input line 16422. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 122 undefined on input line 16422. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 122 undefi ned on input line 16422. [122] [123] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 124 undefined on input line 16556. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 124 undefi ned on input line 16556. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 124 undefined on input line 16556. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 124 undefi ned on input line 16556. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 124 undefined on input line 16556. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 124 undefi ned on input line 16556. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 124 undefined on input line 16556. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 124 undefi ned on input line 16556. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 124 undefined on input line 16602. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 124 undefi ned on input line 16602. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 124 undefined on input line 16608. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 124 undefi ned on input line 16608. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 124 undefined on input line 16644. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 124 undefi ned on input line 16644. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 124 undefined on input line 16646. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 124 undefi ned on input line 16646. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 124 undefined on input line 16647. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 124 undefi ned on input line 16647. [124] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 125 undefined on input line 16653. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 125 undefi ned on input line 16653. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 125 undefined on input line 16771. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 125 undefi ned on input line 16771. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 125 undefined on input line 16771. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 125 undefi ned on input line 16771. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 125 undefined on input line 16771. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 125 undefi ned on input line 16771. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 125 undefined on input line 16771. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 125 undefi ned on input line 16771. [125] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 126 undefined on input line 16850. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 126 undefi ned on input line 16850. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 126 undefined on input line 16863. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 126 undefi ned on input line 16863. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 126 undefined on input line 16867. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 126 undefi ned on input line 16867. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 126 undefined on input line 16867. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 126 undefi ned on input line 16867. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 126 undefined on input line 16867. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 126 undefi ned on input line 16867. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 126 undefined on input line 16867. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 126 undefi ned on input line 16867. [126] [127] LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 128 undefined on input line 16972. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 128 undefi ned on input line 16972. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 128 undefined on input line 16972. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 128 undefi ned on input line 16972. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 128 undefined on input line 16973. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 128 undefi ned on input line 16973. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 128 undefined on input line 16973. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 128 undefi ned on input line 16973. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 128 undefined on input line 16974. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 128 undefi ned on input line 16974. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 128 undefined on input line 16990. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 128 undefi ned on input line 16990. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 128 undefined on input line 16998. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 128 undefi ned on input line 16998. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 128 undefined on input line 17020. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 128 undefi ned on input line 17020. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 128 undefined on input line 17024. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 128 undefi ned on input line 17024. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 128 undefined on input line 17036. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 128 undefi ned on input line 17036. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 128 undefined on input line 17036. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 128 undefi ned on input line 17036. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 128 undefined on input line 17036. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 128 undefi ned on input line 17036. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 128 undefined on input line 17036. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 128 undefi ned on input line 17036. [128] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 129 undefined on input line 17178. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 129 undefi ned on input line 17178. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 129 undefined on input line 17179. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 129 undefi ned on input line 17179. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 129 undefined on input line 17184. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 129 undefi ned on input line 17184. [129] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 130 undefined on input line 17214. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 130 undefi ned on input line 17214. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 130 undefined on input line 17214. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 130 undefi ned on input line 17214. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 130 undefined on input line 17214. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 130 undefi ned on input line 17214. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 130 undefined on input line 17214. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 130 undefi ned on input line 17214. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 130 undefined on input line 17218. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 130 undefi ned on input line 17218. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 130 undefined on input line 17284. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 130 undefi ned on input line 17284. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 130 undefined on input line 17284. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 130 undefi ned on input line 17284. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 130 undefined on input line 17284. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 130 undefi ned on input line 17284. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 130 undefined on input line 17284. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 130 undefi ned on input line 17284. [130] LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 131 undefined on input line 17352. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 131 undefi ned on input line 17352. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 131 undefined on input line 17356. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 131 undefi ned on input line 17356. [131] LaTeX Warning: Hyper reference `onlinehelp/gmx-rama::doc' on page 132 undefined on input line 17401. LaTeX Warning: Reference `onlinehelp/gmx-rama::doc' on page 132 undefined on in put line 17401. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 132 undefined on input line 17442. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 132 undefi ned on input line 17442. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 132 undefined on input line 17467. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 132 undefi ned on input line 17467. [132] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 133 undefined on input line 17562. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 133 undefi ned on input line 17562. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 133 undefined on input line 17566. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 133 undefi ned on input line 17566. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 133 undefined on input line 17566. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 133 undefi ned on input line 17566. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 133 undefined on input line 17566. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 133 undefi ned on input line 17566. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 133 undefined on input line 17566. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 133 undefi ned on input line 17566. [133] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 134 undefined on input line 17623. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 134 undefi ned on input line 17623. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 134 undefined on input line 17652. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 134 undefi ned on input line 17652. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 134 undefined on input line 17652. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 134 undefi ned on input line 17652. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 134 undefined on input line 17652. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 134 undefi ned on input line 17652. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 134 undefined on input line 17652. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 134 undefi ned on input line 17652. [134] LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 135 undefined on input line 17704. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 135 undefi ned on input line 17704. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 135 undefined on input line 17763. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 135 undefi ned on input line 17763. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 135 undefined on input line 17764. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 135 undefi ned on input line 17764. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 135 undefined on input line 17774. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 135 undefi ned on input line 17774. [135] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 136 undefined on input line 17793. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 136 undefi ned on input line 17793. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 136 undefined on input line 17863. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 136 undefi ned on input line 17863. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 136 undefined on input line 17863. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 136 undefi ned on input line 17863. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 136 undefined on input line 17863. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 136 undefi ned on input line 17863. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 136 undefined on input line 17863. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 136 undefi ned on input line 17863. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 136 undefined on input line 17875. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 136 undefi ned on input line 17875. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 136 undefined on input line 17887. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 136 undefi ned on input line 17887. [136] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17930. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17930. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17932. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17932. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 137 undefined on input line 17943. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 137 undefi ned on input line 17943. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 137 undefined on input line 17943. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 137 undefi ned on input line 17943. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 137 undefined on input line 17943. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 137 undefi ned on input line 17943. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17943. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17943. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 137 undefined on input line 17947. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 137 undefi ned on input line 17947. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 137 undefined on input line 17947. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 137 undefi ned on input line 17947. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17947. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17947. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 137 undefined on input line 17947. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 137 undefi ned on input line 17947. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 137 undefined on input line 17964. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 137 undefi ned on input line 17964. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 137 undefined on input line 17964. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 137 undefi ned on input line 17964. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17964. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17964. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 137 undefined on input line 17977. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 137 undefi ned on input line 17977. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 137 undefined on input line 17977. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 137 undefi ned on input line 17977. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 137 undefined on input line 17977. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 137 undefi ned on input line 17977. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 137 undefined on input line 17977. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 137 undefi ned on input line 17977. [137] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 138 undefined on input line 18056. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 138 undefi ned on input line 18056. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 138 undefined on input line 18056. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 138 undefi ned on input line 18056. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 138 undefined on input line 18056. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 138 undefi ned on input line 18056. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 138 undefined on input line 18056. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 138 undefi ned on input line 18056. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 138 undefined on input line 18069. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 138 undefi ned on input line 18069. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 138 undefined on input line 18069. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 138 undefi ned on input line 18069. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 138 undefined on input line 18069. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 138 undefi ned on input line 18069. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 138 undefined on input line 18069. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 138 undefi ned on input line 18069. [138] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 139 undefined on input line 18146. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 139 undefi ned on input line 18146. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 139 undefined on input line 18150. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 139 undefi ned on input line 18150. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 139 undefined on input line 18150. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 139 undefi ned on input line 18150. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 139 undefined on input line 18150. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 139 undefi ned on input line 18150. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 139 undefined on input line 18150. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 139 undefi ned on input line 18150. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 139 undefi ned on input line 18163. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 139 undefined on input line 18163. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 139 undefi ned on input line 18163. [139] LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig::doc' on page 140 undefin ed on input line 18281. LaTeX Warning: Reference `onlinehelp/gmx-anaeig::doc' on page 140 undefined on input line 18281. [140] LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 141 undefined on input line 18288. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 141 undefi ned on input line 18288. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 141 undefined on input line 18291. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 141 undefi ned on input line 18291. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 141 undefined on input line 18311. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 141 undefi ned on input line 18311. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 141 undefined on input line 18315. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 141 undefi ned on input line 18315. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 141 undefined on input line 18315. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 141 undefi ned on input line 18315. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 141 undefined on input line 18315. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 141 undefi ned on input line 18315. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 141 undefined on input line 18315. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 141 undefi ned on input line 18315. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 141 undefined on input line 18332. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 141 undefi ned on input line 18332. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 141 undefined on input line 18332. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 141 undefi ned on input line 18332. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 141 undefined on input line 18332. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 141 undefi ned on input line 18332. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 141 undefined on input line 18336. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 141 undefi ned on input line 18336. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 141 undefined on input line 18336. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 141 undefi ned on input line 18336. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 141 undefined on input line 18336. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 141 undefi ned on input line 18336. [141] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 142 undefined on input line 18467. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 142 undefi ned on input line 18467. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 142 undefined on input line 18467. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 142 undefi ned on input line 18467. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 142 undefined on input line 18467. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 142 undefi ned on input line 18467. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 142 undefined on input line 18467. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 142 undefi ned on input line 18467. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 142 undefi ned on input line 18475. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 142 undefined on input line 18475. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 142 undefi ned on input line 18475. [142] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 143 undefined on input line 18525. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 143 undefi ned on input line 18525. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 143 undefined on input line 18525. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 143 undefi ned on input line 18525. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 143 undefined on input line 18525. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 143 undefi ned on input line 18525. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 143 undefined on input line 18525. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 143 undefi ned on input line 18525. [143] LaTeX Warning: Hyper reference `onlinehelp/gmx-energy::doc' on page 144 undefin ed on input line 18587. LaTeX Warning: Reference `onlinehelp/gmx-energy::doc' on page 144 undefined on input line 18587. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 144 undefi ned on input line 18659. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 144 undefined on input line 18659. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 144 undefi ned on input line 18659. [144] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 145 undefined on input line 18701. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 145 undefi ned on input line 18701. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 145 undefined on input line 18701. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 145 undefi ned on input line 18701. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 145 undefined on input line 18701. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 145 undefi ned on input line 18701. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 145 undefined on input line 18701. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 145 undefi ned on input line 18701. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 145 undefined on input line 18764. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 145 undefi ned on input line 18764. LaTeX Warning: Hyper reference `reference-manual/file-formats:dat' on page 145 undefined on input line 18766. LaTeX Warning: Reference `reference-manual/file-formats:dat' on page 145 undefi ned on input line 18766. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 145 undefined on input line 18767. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 145 undefi ned on input line 18767. [145] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 146 undefined on input line 18807. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 146 undefi ned on input line 18807. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 146 undefined on input line 18811. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 146 undefi ned on input line 18811. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 146 undefined on input line 18811. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 146 undefi ned on input line 18811. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 146 undefined on input line 18811. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 146 undefi ned on input line 18811. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 146 undefined on input line 18811. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 146 undefi ned on input line 18811. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 146 undefined on input line 18849. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 146 undefi ned on input line 18849. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 146 undefined on input line 18849. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 146 undefi ned on input line 18849. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 146 undefined on input line 18849. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 146 undefi ned on input line 18849. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 146 undefined on input line 18849. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 146 undefi ned on input line 18849. [146] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 147 undefi ned on input line 18945. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 147 undefined on input line 18945. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 147 undefi ned on input line 18945. [147] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 148 undefined on input line 18991. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 148 undefi ned on input line 18991. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 148 undefined on input line 18991. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 148 undefi ned on input line 18991. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 148 undefined on input line 18991. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 148 undefi ned on input line 18991. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 148 undefined on input line 18991. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 148 undefi ned on input line 18991. LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles::doc' on page 148 undefi ned on input line 19057. LaTeX Warning: Reference `onlinehelp/gmx-dipoles::doc' on page 148 undefined on input line 19057. [148] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 149 undefined on input line 19137. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 149 undefi ned on input line 19137. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 149 undefined on input line 19137. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 149 undefi ned on input line 19137. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 149 undefined on input line 19137. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 149 undefi ned on input line 19137. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 149 undefined on input line 19137. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 149 undefi ned on input line 19137. [149] [150] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 151 undefined on input line 19284. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 151 undefi ned on input line 19284. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 151 undefined on input line 19362. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 151 undefi ned on input line 19362. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 151 undefined on input line 19362. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 151 undefi ned on input line 19362. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 151 undefined on input line 19362. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 151 undefi ned on input line 19362. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 151 undefined on input line 19362. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 151 undefi ned on input line 19362. [151] LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 152 undefined on input line 19426. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 152 undefi ned on input line 19426. [152] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 153 undefined on input line 19494. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 153 undefi ned on input line 19494. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 153 undefi ned on input line 19516. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 153 undefined on input line 19516. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 153 undefi ned on input line 19516. [153] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 154 undefined on input line 19582. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 154 undefi ned on input line 19582. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 154 undefined on input line 19582. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 154 undefi ned on input line 19582. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 154 undefined on input line 19582. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 154 undefi ned on input line 19582. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 154 undefined on input line 19582. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 154 undefi ned on input line 19582. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist::doc' on page 154 undef ined on input line 19650. LaTeX Warning: Reference `onlinehelp/gmx-pairdist::doc' on page 154 undefined o n input line 19650. [154] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 155 undefined on input line 19660. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 155 undefi ned on input line 19660. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 155 undefined on input line 19664. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 155 undefi ned on input line 19664. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 155 undefined on input line 19664. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 155 undefi ned on input line 19664. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 155 undefined on input line 19664. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 155 undefi ned on input line 19664. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 155 undefined on input line 19664. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 155 undefi ned on input line 19664. [155] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 156 undefined on input line 19802. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 156 undefi ned on input line 19802. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 156 undefined on input line 19802. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 156 undefi ned on input line 19802. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 156 undefined on input line 19802. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 156 undefi ned on input line 19802. [156] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 157 undefined on input line 19852. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 157 undefi ned on input line 19852. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 157 undefined on input line 19852. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 157 undefi ned on input line 19852. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 157 undefined on input line 19852. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 157 undefi ned on input line 19852. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 157 undefined on input line 19852. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 157 undefi ned on input line 19852. [157] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 158 undefined on input line 20011. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 158 undefi ned on input line 20011. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 158 undefined on input line 20015. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 158 undefi ned on input line 20015. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 158 undefined on input line 20015. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 158 undefi ned on input line 20015. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 158 undefined on input line 20015. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 158 undefi ned on input line 20015. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 158 undefined on input line 20015. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 158 undefi ned on input line 20015. [158] [159] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 160 undefined on input line 20138. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 160 undefi ned on input line 20138. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 160 undefined on input line 20139. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 160 undefi ned on input line 20139. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 160 undefined on input line 20139. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 160 undefi ned on input line 20139. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 160 undefined on input line 20140. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 160 undefi ned on input line 20140. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 160 undefined on input line 20140. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 160 undefi ned on input line 20140. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 160 undefined on input line 20141. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 160 undefi ned on input line 20141. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 160 undefi ned on input line 20158. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 160 undefined on input line 20158. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 160 undefi ned on input line 20158. [160] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 161 undefined on input line 20213. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 161 undefi ned on input line 20213. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 161 undefi ned on input line 20261. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 161 undefined on input line 20261. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 161 undefi ned on input line 20261. [161] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 162 undefined on input line 20311. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 162 undefi ned on input line 20311. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 162 undefined on input line 20311. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 162 undefi ned on input line 20311. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 162 undefined on input line 20311. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 162 undefi ned on input line 20311. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 162 undefined on input line 20311. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 162 undefi ned on input line 20311. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 162 undefined on input line 20359. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 162 undefi ned on input line 20359. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 162 undefined on input line 20360. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 162 undefi ned on input line 20360. [162] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 163 undefined on input line 20415. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 163 undefi ned on input line 20415. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20430. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20430. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20442. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20442. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20460. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20460. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 163 undefined on input line 20481. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 163 undefi ned on input line 20481. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 163 undefined on input line 20481. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 163 undefi ned on input line 20481. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20481. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20481. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 163 undefined on input line 20481. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 163 undefi ned on input line 20481. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 163 undefined on input line 20498. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 163 undefi ned on input line 20498. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 163 undefined on input line 20498. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 163 undefi ned on input line 20498. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20498. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20498. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 163 undefined on input line 20511. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 163 undefi ned on input line 20511. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 163 undefined on input line 20511. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 163 undefi ned on input line 20511. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 163 undefined on input line 20511. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 163 undefi ned on input line 20511. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 163 undefined on input line 20511. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 163 undefi ned on input line 20511. [163] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 164 undefined on input line 20607. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 164 undefi ned on input line 20607. [164] LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 165 undefi ned on input line 20620. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 165 undefined on input line 20620. [165] [166] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 167 undefined on input line 20844. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 167 undefi ned on input line 20844. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 167 undefined on input line 20844. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 167 undefi ned on input line 20844. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 167 undefined on input line 20844. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 167 undefi ned on input line 20844. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 167 undefined on input line 20844. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 167 undefi ned on input line 20844. [167] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 168 undefined on input line 20946. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 168 undefi ned on input line 20946. LaTeX Warning: Hyper reference `onlinehelp/gmx-dos::doc' on page 168 undefined on input line 21016. LaTeX Warning: Reference `onlinehelp/gmx-dos::doc' on page 168 undefined on inp ut line 21016. [168] [169] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 170 undefined on input line 21153. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 170 undefi ned on input line 21153. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 170 undefined on input line 21153. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 170 undefi ned on input line 21153. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 170 undefined on input line 21153. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 170 undefi ned on input line 21153. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 170 undefined on input line 21153. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 170 undefi ned on input line 21153. [170] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 171 undefined on input line 21294. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 171 undefi ned on input line 21294. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 171 undefined on input line 21298. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 171 undefi ned on input line 21298. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 171 undefined on input line 21298. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 171 undefi ned on input line 21298. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 171 undefined on input line 21298. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 171 undefi ned on input line 21298. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 171 undefined on input line 21298. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 171 undefi ned on input line 21298. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 171 undefi ned on input line 21315. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 171 undefined on input line 21315. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 171 undefi ned on input line 21315. [171] [172] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 173 undefined on input line 21446. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 173 undefi ned on input line 21446. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 173 undefined on input line 21450. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 173 undefi ned on input line 21450. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 173 undefined on input line 21450. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 173 undefi ned on input line 21450. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 173 undefined on input line 21450. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 173 undefi ned on input line 21450. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 173 undefined on input line 21450. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 173 undefi ned on input line 21450. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 173 undefined on input line 21463. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 173 undefi ned on input line 21463. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 173 undefined on input line 21467. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 173 undefi ned on input line 21467. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 173 undefined on input line 21488. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 173 undefi ned on input line 21488. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 173 undefined on input line 21488. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 173 undefi ned on input line 21488. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 173 undefined on input line 21488. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 173 undefi ned on input line 21488. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 173 undefined on input line 21488. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 173 undefi ned on input line 21488. [173] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 174 undefined on input line 21571. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 174 undefi ned on input line 21571. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 174 undefined on input line 21575. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 174 undefi ned on input line 21575. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 174 undefined on input line 21575. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 174 undefi ned on input line 21575. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 174 undefined on input line 21575. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 174 undefi ned on input line 21575. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 174 undefined on input line 21575. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 174 undefi ned on input line 21575. [174] [175] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 176 undefined on input line 21739. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 176 undefi ned on input line 21739. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 176 undefined on input line 21743. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 176 undefi ned on input line 21743. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 176 undefined on input line 21743. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 176 undefi ned on input line 21743. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 176 undefined on input line 21743. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 176 undefi ned on input line 21743. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 176 undefined on input line 21743. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 176 undefi ned on input line 21743. [176] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 177 undefined on input line 21880. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 177 undefi ned on input line 21880. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 177 undefined on input line 21880. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 177 undefi ned on input line 21880. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 177 undefined on input line 21880. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 177 undefi ned on input line 21880. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 177 undefined on input line 21880. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 177 undefi ned on input line 21880. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 177 undefined on input line 21884. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 177 undefi ned on input line 21884. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 177 undefined on input line 21893. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 177 undefi ned on input line 21893. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 177 undefined on input line 21893. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 177 undefi ned on input line 21893. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 177 undefined on input line 21893. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 177 undefi ned on input line 21893. [177] LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules::doc' on page 1 78 undefined on input line 21971. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules::doc' on page 178 und efined on input line 21971. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 178 undefined on input line 22003. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 178 undefi ned on input line 22003. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 178 undefined on input line 22003. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 178 undefi ned on input line 22003. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 178 undefined on input line 22003. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 178 undefi ned on input line 22003. [178] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 179 undefined on input line 22044. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 179 undefi ned on input line 22044. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 179 undefined on input line 22100. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 179 undefi ned on input line 22100. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 179 undefined on input line 22117. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 179 undefi ned on input line 22117. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 179 undefined on input line 22117. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 179 undefi ned on input line 22117. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 179 undefined on input line 22117. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 179 undefi ned on input line 22117. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 179 undefined on input line 22117. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 179 undefi ned on input line 22117. [179] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 180 undefine d on input line 22206. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 180 undefined on i nput line 22206. [180] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 181 undefined on input line 22235. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 181 undefi ned on input line 22235. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 181 undefined on input line 22260. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 181 undefi ned on input line 22260. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr::doc' on page 181 un defined on input line 22268. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr::doc' on page 181 undefine d on input line 22268. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 181 undefine d on input line 22269. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 181 undefined on i nput line 22269. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 181 undefined on input line 22272. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 181 undefi ned on input line 22272. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 181 undefine d on input line 22275. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 181 undefined on i nput line 22275. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump::doc' on page 181 undefined on input line 22293. LaTeX Warning: Reference `onlinehelp/gmx-dump::doc' on page 181 undefined on in put line 22293. LaTeX Warning: Hyper reference `onlinehelp/gmx-check::doc' on page 181 undefine d on input line 22294. LaTeX Warning: Reference `onlinehelp/gmx-check::doc' on page 181 undefined on i nput line 22294. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 181 undefined on input line 22316. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 181 undefi ned on input line 22316. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 181 undefined on input line 22316. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 181 undefi ned on input line 22316. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 181 undefined on input line 22316. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 181 undefi ned on input line 22316. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 181 undefined on input line 22316. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 181 undefi ned on input line 22316. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 181 undefined on input line 22320. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 181 undefi ned on input line 22320. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 181 undefined on input line 22320. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 181 undefi ned on input line 22320. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 181 undefined on input line 22320. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 181 undefi ned on input line 22320. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 181 undefined on input line 22320. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 181 undefi ned on input line 22320. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 181 undefined on input line 22324. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 181 undefi ned on input line 22324. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 181 undefined on input line 22324. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 181 undefi ned on input line 22324. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 181 undefined on input line 22324. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 181 undefi ned on input line 22324. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 181 undefined on input line 22324. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 181 undefi ned on input line 22324. [181] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 182 undefined on input line 22336. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 182 undefi ned on input line 22336. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 182 undefined on input line 22336. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 182 undefi ned on input line 22336. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 182 undefined on input line 22336. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 182 undefi ned on input line 22336. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 182 undefined on input line 22353. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 182 undefi ned on input line 22353. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 182 undefined on input line 22353. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 182 undefi ned on input line 22353. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 182 undefined on input line 22353. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 182 undefi ned on input line 22353. [182] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 183 undefined on input line 22452. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 183 undefi ned on input line 22452. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 183 undefined on input line 22456. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 183 undefi ned on input line 22456. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 183 undefined on input line 22456. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 183 undefi ned on input line 22456. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 183 undefined on input line 22456. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 183 undefi ned on input line 22456. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 183 undefined on input line 22456. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 183 undefi ned on input line 22456. [183] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 184 undefined on input line 22574. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 184 undefi ned on input line 22574. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 184 undefined on input line 22578. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 184 undefi ned on input line 22578. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 184 undefined on input line 22578. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 184 undefi ned on input line 22578. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 184 undefined on input line 22578. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 184 undefi ned on input line 22578. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 184 undefined on input line 22578. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 184 undefi ned on input line 22578. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 184 undefined on input line 22616. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 184 undefi ned on input line 22616. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 184 undefined on input line 22616. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 184 undefi ned on input line 22616. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 184 undefined on input line 22616. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 184 undefi ned on input line 22616. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 184 undefined on input line 22616. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 184 undefi ned on input line 22616. [184] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 185 undefi ned on input line 22703. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 185 undefined on input line 22703. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 185 undefi ned on input line 22703. [185] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 186 undefined on input line 22745. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 186 undefi ned on input line 22745. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 186 undefined on input line 22745. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 186 undefi ned on input line 22745. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 186 undefined on input line 22745. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 186 undefi ned on input line 22745. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 186 undefined on input line 22745. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 186 undefi ned on input line 22745. [186] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 187 undefined on input line 22845. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 187 undefi ned on input line 22845. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 187 undefined on input line 22849. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 187 undefi ned on input line 22849. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 187 undefined on input line 22849. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 187 undefi ned on input line 22849. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 187 undefined on input line 22849. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 187 undefi ned on input line 22849. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 187 undefined on input line 22849. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 187 undefi ned on input line 22849. [187] [188] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 189 undefi ned on input line 23089. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 189 undefined on input line 23089. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 189 undefi ned on input line 23089. [189] [190] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 191 undefined on input line 23227. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 191 undefi ned on input line 23227. [191] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 192 undefined on input line 23354. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 192 undefi ned on input line 23354. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 192 undefined on input line 23363. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 192 undefi ned on input line 23363. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 192 undefined on input line 23363. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 192 undefi ned on input line 23363. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 192 undefined on input line 23363. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 192 undefi ned on input line 23363. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 192 undefined on input line 23384. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 192 undefi ned on input line 23384. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 192 undefined on input line 23384. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 192 undefi ned on input line 23384. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 192 undefined on input line 23384. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 192 undefi ned on input line 23384. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 192 undefined on input line 23384. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 192 undefi ned on input line 23384. [192] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 193 undefi ned on input line 23474. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 193 undefined on input line 23474. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 193 undefi ned on input line 23474. [193] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 194 undefi ned on input line 23592. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 194 undefined on input line 23592. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 194 undefi ned on input line 23592. [194] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 195 undefined on input line 23638. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 195 undefi ned on input line 23638. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 195 undefined on input line 23638. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 195 undefi ned on input line 23638. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 195 undefined on input line 23638. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 195 undefi ned on input line 23638. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 195 undefined on input line 23638. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 195 undefi ned on input line 23638. [195] LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 196 undef ined on input line 23729. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 196 undefined o n input line 23729. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 196 undefined on input line 23742. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 196 undefi ned on input line 23742. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 196 undefined on input line 23742. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 196 undefi ned on input line 23742. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 196 undefined on input line 23742. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 196 undefi ned on input line 23742. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 196 undefined on input line 23742. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 196 undefi ned on input line 23742. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 196 undefined on input line 23746. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 196 undefi ned on input line 23746. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 196 undefined on input line 23746. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 196 undefi ned on input line 23746. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 196 undefined on input line 23746. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 196 undefi ned on input line 23746. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 196 undefined on input line 23746. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 196 undefi ned on input line 23746. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 196 undefined on input line 23763. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 196 undefi ned on input line 23763. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 196 undefined on input line 23763. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 196 undefi ned on input line 23763. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 196 undefined on input line 23763. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 196 undefi ned on input line 23763. [196] LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 197 undefined on input line 23845. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 197 undefi ned on input line 23845. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 197 undefined on input line 23886. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 197 undefi ned on input line 23886. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 197 undefined on input line 23886. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 197 undefi ned on input line 23886. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 197 undefined on input line 23886. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 197 undefi ned on input line 23886. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 197 undefined on input line 23886. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 197 undefi ned on input line 23886. [197] LaTeX Warning: Hyper reference `onlinehelp/gmx-covar::doc' on page 198 undefine d on input line 23941. LaTeX Warning: Reference `onlinehelp/gmx-covar::doc' on page 198 undefined on i nput line 23941. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig::doc' on page 198 undefine d on input line 23942. LaTeX Warning: Reference `onlinehelp/gmx-nmeig::doc' on page 198 undefined on i nput line 23942. [198] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 199 undefined on input line 24005. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 199 undefi ned on input line 24005. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 199 undefined on input line 24027. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 199 undefi ned on input line 24027. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 199 undefined on input line 24034. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 199 undefi ned on input line 24034. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 199 undefined on input line 24038. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 199 undefi ned on input line 24038. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 199 undefined on input line 24040. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 199 undefi ned on input line 24040. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 199 undefined on input line 24040. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 199 undefi ned on input line 24040. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 199 undefined on input line 24088. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 199 undefi ned on input line 24088. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 199 undefined on input line 24099. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 199 undefi ned on input line 24099. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 199 undefined on input line 24099. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 199 undefi ned on input line 24099. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 199 undefined on input line 24099. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 199 undefi ned on input line 24099. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 199 undefined on input line 24107. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 199 undefi ned on input line 24107. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 199 undefined on input line 24107. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 199 undefi ned on input line 24107. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 199 undefined on input line 24107. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 199 undefi ned on input line 24107. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 199 undefined on input line 24107. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 199 undefi ned on input line 24107. [199] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 200 undefined on input line 24115. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 200 undefi ned on input line 24115. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 200 undefined on input line 24115. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 200 undefi ned on input line 24115. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 200 undefined on input line 24115. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 200 undefi ned on input line 24115. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 200 undefined on input line 24115. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 200 undefi ned on input line 24115. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 200 undefined on input line 24119. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 200 undefi ned on input line 24119. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 200 undefined on input line 24119. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 200 undefi ned on input line 24119. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 200 undefined on input line 24119. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 200 undefi ned on input line 24119. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 200 undefined on input line 24119. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 200 undefi ned on input line 24119. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 200 undefined on input line 24169. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 200 undefi ned on input line 24169. [200] LaTeX Warning: Hyper reference `onlinehelp/gmx-select::doc' on page 201 undefin ed on input line 24279. LaTeX Warning: Reference `onlinehelp/gmx-select::doc' on page 201 undefined on input line 24279. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 201 undefined on input line 24291. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 201 undefi ned on input line 24291. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 201 undefined on input line 24291. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 201 undefi ned on input line 24291. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 201 undefined on input line 24291. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 201 undefi ned on input line 24291. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 201 undefined on input line 24291. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 201 undefi ned on input line 24291. [201] LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps::doc' on page 202 undefin ed on input line 24347. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps::doc' on page 202 undefined on input line 24347. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 202 undefined on input line 24357. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 202 undefi ned on input line 24357. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 202 undefined on input line 24361. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 202 undefi ned on input line 24361. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 202 undefined on input line 24361. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 202 undefi ned on input line 24361. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 202 undefined on input line 24361. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 202 undefi ned on input line 24361. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 202 undefined on input line 24361. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 202 undefi ned on input line 24361. [202] LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig::doc' on page 203 undefine d on input line 24459. LaTeX Warning: Reference `onlinehelp/gmx-nmeig::doc' on page 203 undefined on i nput line 24459. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 203 undefined on input line 24487. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 203 undefi ned on input line 24487. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 203 undefined on input line 24488. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 203 undefi ned on input line 24488. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 203 undefined on input line 24490. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 203 undefi ned on input line 24490. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 203 undefined on input line 24496. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 203 undefi ned on input line 24496. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 203 undefined on input line 24518. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 203 undefi ned on input line 24518. [203] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 204 undefined on input line 24547. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 204 undefi ned on input line 24547. [204] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 205 undefined on input line 24632. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 205 undefi ned on input line 24632. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 205 undefined on input line 24669. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 205 undefi ned on input line 24669. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 205 undefined on input line 24669. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 205 undefi ned on input line 24669. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 205 undefined on input line 24669. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 205 undefi ned on input line 24669. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 205 undefined on input line 24681. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 205 undefi ned on input line 24681. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 205 undefined on input line 24681. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 205 undefi ned on input line 24681. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 205 undefined on input line 24681. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 205 undefi ned on input line 24681. [205] [206] [207] LaTeX Warning: Hyper reference `onlinehelp/gmx-distance::doc' on page 208 undef ined on input line 24945. LaTeX Warning: Reference `onlinehelp/gmx-distance::doc' on page 208 undefined o n input line 24945. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist::doc' on page 208 undef ined on input line 24945. LaTeX Warning: Reference `onlinehelp/gmx-pairdist::doc' on page 208 undefined o n input line 24945. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 208 undefined on input line 24955. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 208 undefi ned on input line 24955. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 208 undefined on input line 24959. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 208 undefi ned on input line 24959. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 208 undefined on input line 24959. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 208 undefi ned on input line 24959. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 208 undefined on input line 24959. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 208 undefi ned on input line 24959. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 208 undefined on input line 24959. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 208 undefi ned on input line 24959. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 208 undefi ned on input line 24984. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 208 undefi ned on input line 24984. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 208 undefi ned on input line 24984. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 208 undefi ned on input line 24984. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 208 undefi ned on input line 24984. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 208 undefined on input line 24984. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 208 undefi ned on input line 24984. [208] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 209 undefined on input line 25013. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 209 undefi ned on input line 25013. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 209 undefined on input line 25013. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 209 undefi ned on input line 25013. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 209 undefined on input line 25013. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 209 undefi ned on input line 25013. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 209 undefined on input line 25013. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 209 undefi ned on input line 25013. [209] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 210 undefined on input line 25193. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 210 undefi ned on input line 25193. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 210 undefined on input line 25197. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 210 undefi ned on input line 25197. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 210 undefined on input line 25197. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 210 undefi ned on input line 25197. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 210 undefined on input line 25197. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 210 undefi ned on input line 25197. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 210 undefined on input line 25197. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 210 undefi ned on input line 25197. [210] [211] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 212 undefine d on input line 25316. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 212 undefined on i nput line 25316. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig::doc' on page 212 undefin ed on input line 25321. LaTeX Warning: Reference `onlinehelp/gmx-anaeig::doc' on page 212 undefined on input line 25321. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmens::doc' on page 212 undefine d on input line 25323. LaTeX Warning: Reference `onlinehelp/gmx-nmens::doc' on page 212 undefined on i nput line 25323. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 212 undefined on input line 25394. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 212 undefi ned on input line 25394. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 212 undefined on input line 25394. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 212 undefi ned on input line 25394. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 212 undefined on input line 25394. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 212 undefi ned on input line 25394. [212] [213] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 214 undefined on input line 25487. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 214 undefi ned on input line 25487. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 214 undefined on input line 25487. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 214 undefi ned on input line 25487. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 214 undefined on input line 25487. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 214 undefi ned on input line 25487. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 214 undefined on input line 25495. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 214 undefi ned on input line 25495. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 214 undefined on input line 25495. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 214 undefi ned on input line 25495. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 214 undefined on input line 25495. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 214 undefi ned on input line 25495. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 214 undefined on input line 25495. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 214 undefi ned on input line 25495. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 214 undefi ned on input line 25508. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 214 undefi ned on input line 25508. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 214 undefi ned on input line 25508. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 214 undefi ned on input line 25508. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 214 undefi ned on input line 25508. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 214 undefined on input line 25508. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 214 undefi ned on input line 25508. [214] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 215 undefined on input line 25662. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 215 undefi ned on input line 25662. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 215 undefined on input line 25662. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 215 undefi ned on input line 25662. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 215 undefined on input line 25662. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 215 undefi ned on input line 25662. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 215 undefined on input line 25662. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 215 undefi ned on input line 25662. [215] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 216 undefined on input line 25732. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 216 undefi ned on input line 25732. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 216 undefined on input line 25732. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 216 undefi ned on input line 25732. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 216 undefined on input line 25732. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 216 undefi ned on input line 25732. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 216 undefined on input line 25732. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 216 undefi ned on input line 25732. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 216 undefined on input line 25736. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 216 undefi ned on input line 25736. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 216 undefined on input line 25736. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 216 undefi ned on input line 25736. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 216 undefined on input line 25736. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 216 undefi ned on input line 25736. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 216 undefi ned on input line 25745. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 216 undefi ned on input line 25745. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 216 undefi ned on input line 25745. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 216 undefi ned on input line 25745. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 216 undefi ned on input line 25745. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 216 undefined on input line 25745. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 216 undefi ned on input line 25745. [216] [217] [218] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 219 undefined on input line 25999. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 219 undefi ned on input line 25999. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 219 undefined on input line 26069. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 219 undefi ned on input line 26069. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 219 undefined on input line 26069. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 219 undefi ned on input line 26069. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 219 undefined on input line 26069. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 219 undefi ned on input line 26069. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 219 undefined on input line 26069. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 219 undefi ned on input line 26069. [219] [220] LaTeX Warning: Hyper reference `onlinehelp/gmx-distance::doc' on page 221 undef ined on input line 26182. LaTeX Warning: Reference `onlinehelp/gmx-distance::doc' on page 221 undefined o n input line 26182. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 221 undefined on input line 26192. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 221 undefi ned on input line 26192. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 221 undefined on input line 26196. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 221 undefi ned on input line 26196. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 221 undefined on input line 26196. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 221 undefi ned on input line 26196. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 221 undefined on input line 26196. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 221 undefi ned on input line 26196. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 221 undefined on input line 26196. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 221 undefi ned on input line 26196. [221] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 222 undefined on input line 26309. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 222 undefi ned on input line 26309. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 222 undefined on input line 26309. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 222 undefi ned on input line 26309. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 222 undefined on input line 26311. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 222 undefi ned on input line 26311. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 222 undefined on input line 26338. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 222 undefi ned on input line 26338. [222] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26389. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26389. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26392. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26392. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 223 undefined on input line 26406. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 223 undefi ned on input line 26406. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26407. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26407. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26408. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26408. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 223 undefined on input line 26445. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 223 undefi ned on input line 26445. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 223 undefined on input line 26445. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 223 undefi ned on input line 26445. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26445. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26445. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 223 undefined on input line 26445. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 223 undefi ned on input line 26445. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 223 undefined on input line 26454. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 223 undefi ned on input line 26454. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 223 undefined on input line 26454. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 223 undefi ned on input line 26454. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26454. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26454. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 223 undefined on input line 26470. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 223 undefi ned on input line 26470. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 223 undefined on input line 26470. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 223 undefi ned on input line 26470. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 223 undefined on input line 26470. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 223 undefi ned on input line 26470. [223] [224] LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 225 undefined on input line 26571. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 225 undefi ned on input line 26571. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 225 undefined on input line 26575. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 225 undefi ned on input line 26575. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 225 undefined on input line 26583. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 225 undefi ned on input line 26583. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 225 undefined on input line 26642. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 225 undefi ned on input line 26642. [225] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 226 undefined on input line 26720. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 226 undefi ned on input line 26720. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 226 undefined on input line 26770. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 226 undefi ned on input line 26770. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 226 undefined on input line 26770. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 226 undefi ned on input line 26770. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 226 undefined on input line 26770. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 226 undefi ned on input line 26770. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 226 undefined on input line 26770. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 226 undefi ned on input line 26770. [226] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 227 undefi ned on input line 26831. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 227 undefined on input line 26831. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 227 undefi ned on input line 26831. [227] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 228 undefined on input line 26877. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 228 undefi ned on input line 26877. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 228 undefined on input line 26877. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 228 undefi ned on input line 26877. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 228 undefined on input line 26877. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 228 undefi ned on input line 26877. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 228 undefined on input line 26877. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 228 undefi ned on input line 26877. [228] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 229 undefined on input line 26968. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 229 undefi ned on input line 26968. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 229 undefined on input line 26972. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 229 undefi ned on input line 26972. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 229 undefined on input line 26972. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 229 undefi ned on input line 26972. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 229 undefined on input line 26972. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 229 undefi ned on input line 26972. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 229 undefined on input line 26972. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 229 undefi ned on input line 26972. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 229 undefined on input line 27022. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 229 undefi ned on input line 27022. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 229 undefined on input line 27022. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 229 undefi ned on input line 27022. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 229 undefined on input line 27022. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 229 undefi ned on input line 27022. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 229 undefined on input line 27022. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 229 undefi ned on input line 27022. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 229 undefi ned on input line 27062. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 229 undefined on input line 27062. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 229 undefi ned on input line 27062. [229] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 230 undefined on input line 27096. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 230 undefi ned on input line 27096. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 230 undefined on input line 27096. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 230 undefi ned on input line 27096. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 230 undefined on input line 27096. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 230 undefi ned on input line 27096. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 230 undefined on input line 27096. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 230 undefi ned on input line 27096. [230] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 231 undefined on input line 27198. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 231 undefi ned on input line 27198. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 231 undefined on input line 27202. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 231 undefi ned on input line 27202. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 231 undefined on input line 27202. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 231 undefi ned on input line 27202. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 231 undefined on input line 27202. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 231 undefi ned on input line 27202. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 231 undefined on input line 27202. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 231 undefi ned on input line 27202. [231] LaTeX Warning: Hyper reference `onlinehelp/gmx-check::doc' on page 232 undefine d on input line 27329. LaTeX Warning: Reference `onlinehelp/gmx-check::doc' on page 232 undefined on i nput line 27329. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 232 undefined on input line 27339. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 232 undefi ned on input line 27339. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 232 undefined on input line 27339. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 232 undefi ned on input line 27339. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 232 undefined on input line 27339. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 232 undefi ned on input line 27339. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 232 undefined on input line 27339. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 232 undefi ned on input line 27339. [232] LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 233 undefined on input line 27401. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 233 undefi ned on input line 27401. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps::doc' on page 233 undefin ed on input line 27404. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps::doc' on page 233 undefined on input line 27404. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 233 undefined on input line 27414. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 233 undefi ned on input line 27414. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 233 undefined on input line 27441. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 233 undefi ned on input line 27441. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 233 undefined on input line 27441. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 233 undefi ned on input line 27441. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 233 undefined on input line 27441. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 233 undefi ned on input line 27441. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 233 undefined on input line 27441. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 233 undefi ned on input line 27441. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 233 undefined on input line 27445. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 233 undefi ned on input line 27445. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 233 undefi ned on input line 27449. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 233 undefined on input line 27449. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 233 undefi ned on input line 27449. [233] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 234 undefined on input line 27511. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 234 undefi ned on input line 27511. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 234 undefined on input line 27511. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 234 undefi ned on input line 27511. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 234 undefined on input line 27511. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 234 undefi ned on input line 27511. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 234 undefined on input line 27511. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 234 undefi ned on input line 27511. [234] LaTeX Warning: Hyper reference `onlinehelp/gmx-rms::doc' on page 235 undefined on input line 27597. LaTeX Warning: Reference `onlinehelp/gmx-rms::doc' on page 235 undefined on inp ut line 27597. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 235 undefined on input line 27630. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 235 undefi ned on input line 27630. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 235 undefined on input line 27634. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 235 undefi ned on input line 27634. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 235 undefined on input line 27634. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 235 undefi ned on input line 27634. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 235 undefined on input line 27634. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 235 undefi ned on input line 27634. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 235 undefined on input line 27634. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 235 undefi ned on input line 27634. [235] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 236 undefined on input line 27696. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 236 undefi ned on input line 27696. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 236 undefined on input line 27696. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 236 undefi ned on input line 27696. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 236 undefined on input line 27696. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 236 undefi ned on input line 27696. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27696. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27696. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27745. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27745. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27746. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27746. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27746. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27746. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27759. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27759. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27765. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27765. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 236 undefined on input line 27768. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 236 undefi ned on input line 27768. [236] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 237 undefined on input line 27783. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 237 undefi ned on input line 27783. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 237 undefined on input line 27787. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 237 undefi ned on input line 27787. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 237 undefined on input line 27787. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 237 undefi ned on input line 27787. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 237 undefined on input line 27787. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 237 undefi ned on input line 27787. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 237 undefined on input line 27787. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 237 undefi ned on input line 27787. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 237 undefined on input line 27845. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 237 undefi ned on input line 27845. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 237 undefined on input line 27845. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 237 undefi ned on input line 27845. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 237 undefined on input line 27845. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 237 undefi ned on input line 27845. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 237 undefined on input line 27845. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 237 undefi ned on input line 27845. [237] Underfull \hbox (badness 10000) in paragraph at lines 27897--27900 []\T1/pcr/m/n/10 gmx rotacf []P 1 []nparm 2 []fft []n index []o rotacf[]x[]P1 [ ]fa expfit[]x[]P1 LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 238 undefined on input line 27915. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 238 undefi ned on input line 27915. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 238 undefined on input line 27953. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 238 undefi ned on input line 27953. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 238 undefined on input line 27953. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 238 undefi ned on input line 27953. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 238 undefined on input line 27953. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 238 undefi ned on input line 27953. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 238 undefined on input line 27953. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 238 undefi ned on input line 27953. [238] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 239 undefined on input line 28047. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 239 undefi ned on input line 28047. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 239 undefined on input line 28051. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 239 undefi ned on input line 28051. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 239 undefined on input line 28051. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 239 undefi ned on input line 28051. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 239 undefined on input line 28051. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 239 undefi ned on input line 28051. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 239 undefined on input line 28051. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 239 undefi ned on input line 28051. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 239 undefined on input line 28085. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 239 undefi ned on input line 28085. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 239 undefined on input line 28085. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 239 undefi ned on input line 28085. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 239 undefined on input line 28085. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 239 undefi ned on input line 28085. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 239 undefined on input line 28085. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 239 undefi ned on input line 28085. [239] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 240 undefi ned on input line 28145. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 240 undefined on input line 28145. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 240 undefi ned on input line 28145. [240] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 241 undefi ned on input line 28246. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 241 undefined on input line 28246. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 241 undefi ned on input line 28246. [241] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 242 undefined on input line 28357. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 242 undefi ned on input line 28357. [242] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 243 undefined on input line 28396. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 243 undefi ned on input line 28396. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 243 undefined on input line 28400. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 243 undefi ned on input line 28400. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 243 undefined on input line 28400. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 243 undefi ned on input line 28400. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 243 undefined on input line 28400. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 243 undefi ned on input line 28400. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 243 undefined on input line 28400. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 243 undefi ned on input line 28400. [243] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 244 undefined on input line 28490. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 244 undefi ned on input line 28490. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 244 undefined on input line 28536. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 244 undefi ned on input line 28536. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 244 undefined on input line 28540. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 244 undefi ned on input line 28540. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 244 undefined on input line 28540. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 244 undefi ned on input line 28540. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 244 undefined on input line 28540. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 244 undefi ned on input line 28540. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 244 undefined on input line 28540. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 244 undefi ned on input line 28540. [244] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 245 undefined on input line 28639. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 245 undefi ned on input line 28639. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 245 undefined on input line 28643. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 245 undefi ned on input line 28643. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 245 undefined on input line 28643. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 245 undefi ned on input line 28643. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 245 undefined on input line 28643. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 245 undefi ned on input line 28643. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 245 undefined on input line 28643. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 245 undefi ned on input line 28643. [245] [246] LaTeX Warning: Hyper reference `onlinehelp/gmx-trajectory::doc' on page 247 und efined on input line 28857. LaTeX Warning: Reference `onlinehelp/gmx-trajectory::doc' on page 247 undefined on input line 28857. [247] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 248 undefined on input line 28867. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 248 undefi ned on input line 28867. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 248 undefined on input line 28871. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 248 undefi ned on input line 28871. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 248 undefined on input line 28871. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 248 undefi ned on input line 28871. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 248 undefined on input line 28871. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 248 undefi ned on input line 28871. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 248 undefined on input line 28871. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 248 undefi ned on input line 28871. [248] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 249 undefined on input line 29014. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 249 undefi ned on input line 29014. [249] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 250 undefined on input line 29122. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 250 undefi ned on input line 29122. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 250 undefined on input line 29122. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 250 undefi ned on input line 29122. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 250 undefined on input line 29122. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 250 undefi ned on input line 29122. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 250 undefined on input line 29122. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 250 undefi ned on input line 29122. [250] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 251 undefined on input line 29242. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 251 undefi ned on input line 29242. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 251 undefined on input line 29242. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 251 undefi ned on input line 29242. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 251 undefined on input line 29242. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 251 undefi ned on input line 29242. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 251 undefined on input line 29242. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 251 undefi ned on input line 29242. [251] LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 252 undef ined on input line 29325. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 252 undefined o n input line 29325. [252] LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 253 undef ined on input line 29360. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 253 undefined o n input line 29360. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 253 undefined on input line 29375. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 253 undefi ned on input line 29375. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 253 undefined on input line 29375. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 253 undefi ned on input line 29375. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 253 undefined on input line 29375. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 253 undefi ned on input line 29375. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 253 undefined on input line 29375. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 253 undefi ned on input line 29375. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 253 undefined on input line 29379. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 253 undefi ned on input line 29379. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 253 undefined on input line 29379. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 253 undefi ned on input line 29379. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 253 undefined on input line 29379. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 253 undefi ned on input line 29379. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 253 undefined on input line 29379. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 253 undefi ned on input line 29379. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 253 undefined on input line 29397. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 253 undefi ned on input line 29397. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 253 undefined on input line 29397. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 253 undefi ned on input line 29397. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 253 undefined on input line 29397. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 253 undefi ned on input line 29397. [253] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 254 undefined on input line 29508. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 254 undefi ned on input line 29508. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 254 undefined on input line 29512. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 254 undefi ned on input line 29512. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 254 undefined on input line 29512. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 254 undefi ned on input line 29512. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 254 undefined on input line 29512. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 254 undefi ned on input line 29512. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 254 undefined on input line 29512. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 254 undefi ned on input line 29512. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 254 undefined on input line 29562. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 254 undefi ned on input line 29562. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 254 undefined on input line 29562. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 254 undefi ned on input line 29562. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 254 undefined on input line 29562. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 254 undefi ned on input line 29562. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 254 undefined on input line 29562. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 254 undefi ned on input line 29562. [254] LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 255 undefi ned on input line 29628. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 255 undefined on input line 29628. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx::doc' on page 255 undef ined on input line 29636. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx::doc' on page 255 undefined o n input line 29636. Underfull \hbox (badness 10000) in paragraph at lines 29639--29641 []\T1/pcr/m/n/10 gmx trjconv []s a.tpr []f a.tng []o b.tng []boxcenter tric []u r compact []pbc [255] LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 256 undefi ned on input line 29666. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 256 undefined on input line 29666. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 256 undefi ned on input line 29681. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 256 undefined on input line 29681. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 256 undefined on input line 29694. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 256 undefi ned on input line 29694. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 256 undefined on input line 29694. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 256 undefi ned on input line 29694. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 256 undefined on input line 29694. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 256 undefi ned on input line 29694. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 256 undefined on input line 29694. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 256 undefi ned on input line 29694. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 256 undefined on input line 29698. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 256 undefi ned on input line 29698. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 256 undefined on input line 29723. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 256 undefi ned on input line 29723. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 256 undefined on input line 29723. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 256 undefi ned on input line 29723. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 256 undefined on input line 29723. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 256 undefi ned on input line 29723. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 256 undefined on input line 29723. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 256 undefi ned on input line 29723. [256] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 257 undefined on input line 29801. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 257 undefi ned on input line 29801. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 257 undefined on input line 29839. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 257 undefi ned on input line 29839. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 257 undefined on input line 29839. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 257 undefi ned on input line 29839. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 257 undefined on input line 29839. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 257 undefi ned on input line 29839. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 257 undefined on input line 29839. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 257 undefi ned on input line 29839. [257] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 258 undefined on input line 29945. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 258 undefi ned on input line 29945. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 258 undefined on input line 29945. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 258 undefi ned on input line 29945. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 258 undefined on input line 29945. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 258 undefi ned on input line 29945. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 258 undefined on input line 29949. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 258 undefi ned on input line 29949. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 258 undefined on input line 29949. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 258 undefi ned on input line 29949. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 258 undefined on input line 29949. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 258 undefi ned on input line 29949. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 258 undefined on input line 29949. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 258 undefi ned on input line 29949. [258] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 259 undefined on input line 30003. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 259 undefi ned on input line 30003. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 259 undefined on input line 30003. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 259 undefi ned on input line 30003. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 259 undefined on input line 30003. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 259 undefi ned on input line 30003. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 259 undefined on input line 30003. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 259 undefi ned on input line 30003. [259] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 260 undefined on input line 30091. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 260 undefi ned on input line 30091. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 260 undefined on input line 30100. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 260 undefi ned on input line 30100. LaTeX Warning: Hyper reference `onlinehelp/gmx-trajectory::doc' on page 260 und efined on input line 30109. LaTeX Warning: Reference `onlinehelp/gmx-trajectory::doc' on page 260 undefined on input line 30109. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 260 undefined on input line 30119. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 260 undefi ned on input line 30119. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 260 undefined on input line 30123. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 260 undefi ned on input line 30123. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 260 undefined on input line 30123. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 260 undefi ned on input line 30123. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 260 undefined on input line 30123. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 260 undefi ned on input line 30123. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 260 undefined on input line 30123. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 260 undefi ned on input line 30123. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 260 undefi ned on input line 30140. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 260 undefined on input line 30140. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 260 undefi ned on input line 30140. [260] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 261 undefined on input line 30209. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 261 undefi ned on input line 30209. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 261 undefined on input line 30209. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 261 undefi ned on input line 30209. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 261 undefined on input line 30209. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 261 undefi ned on input line 30209. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 261 undefined on input line 30209. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 261 undefi ned on input line 30209. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 261 undefined on input line 30265. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 261 undefi ned on input line 30265. [261] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 262 undefined on input line 30307. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 262 undefi ned on input line 30307. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 262 undefined on input line 30311. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 262 undefi ned on input line 30311. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 262 undefined on input line 30311. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 262 undefi ned on input line 30311. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 262 undefined on input line 30311. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 262 undefi ned on input line 30311. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 262 undefined on input line 30311. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 262 undefi ned on input line 30311. [262] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 263 undefined on input line 30440. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 263 undefi ned on input line 30440. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 263 undefined on input line 30441. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 263 undefi ned on input line 30441. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 263 undefined on input line 30453. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 263 undefi ned on input line 30453. [263] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 264 undefined on input line 30464. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 264 undefi ned on input line 30464. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 264 undefi ned on input line 30481. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 264 undefi ned on input line 30481. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 264 undefi ned on input line 30481. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 264 undefi ned on input line 30481. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 264 undefi ned on input line 30481. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 264 undefined on input line 30481. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 264 undefi ned on input line 30481. [264] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 265 undefined on input line 30593. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 265 undefi ned on input line 30593. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjcat::doc' on page 265 undefin ed on input line 30603. LaTeX Warning: Reference `onlinehelp/gmx-trjcat::doc' on page 265 undefined on input line 30603. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 265 undefined on input line 30607. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 265 undefi ned on input line 30607. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 265 undefined on input line 30607. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 265 undefi ned on input line 30607. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 265 undefined on input line 30607. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 265 undefi ned on input line 30607. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 265 undefined on input line 30608. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 265 undefi ned on input line 30608. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 265 undefined on input line 30608. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 265 undefi ned on input line 30608. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 265 undefined on input line 30610. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 265 undefi ned on input line 30610. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 265 undefined on input line 30611. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 265 undefi ned on input line 30611. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 265 undefined on input line 30611. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 265 undefi ned on input line 30611. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 265 undefined on input line 30611. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 265 undefi ned on input line 30611. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 265 undefined on input line 30614. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 265 undefi ned on input line 30614. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 265 undefined on input line 30618. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 265 undefi ned on input line 30618. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 265 undefined on input line 30618. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 265 undefi ned on input line 30618. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 265 undefined on input line 30618. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 265 undefi ned on input line 30618. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 265 undefined on input line 30622. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 265 undefi ned on input line 30622. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 265 undefined on input line 30624. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 265 undefi ned on input line 30624. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 265 undefined on input line 30632. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 265 undefi ned on input line 30632. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 265 undefined on input line 30633. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 265 undefi ned on input line 30633. [265] LaTeX Warning: Hyper reference `onlinehelp/gmx-filter::doc' on page 266 undefin ed on input line 30732. LaTeX Warning: Reference `onlinehelp/gmx-filter::doc' on page 266 undefined on input line 30732. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 266 undefined on input line 30737. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 266 undefi ned on input line 30737. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 266 undefined on input line 30748. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 266 undefi ned on input line 30748. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 266 undefined on input line 30761. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 266 undefi ned on input line 30761. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 266 undefined on input line 30765. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 266 undefi ned on input line 30765. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 266 undefined on input line 30765. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 266 undefi ned on input line 30765. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 266 undefined on input line 30765. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 266 undefi ned on input line 30765. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 266 undefined on input line 30765. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 266 undefi ned on input line 30765. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 266 undefi ned on input line 30790. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 266 undefi ned on input line 30790. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 266 undefi ned on input line 30790. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 266 undefi ned on input line 30790. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 266 undefi ned on input line 30790. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 266 undefined on input line 30790. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 266 undefi ned on input line 30790. [266] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 267 undefined on input line 30811. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 267 undefi ned on input line 30811. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 267 undefined on input line 30811. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 267 undefi ned on input line 30811. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 267 undefined on input line 30811. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 267 undefi ned on input line 30811. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 267 undefined on input line 30811. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 267 undefi ned on input line 30811. [267] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 268 undefined on input line 30915. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 268 undefi ned on input line 30915. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 268 undefined on input line 30958. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 268 undefi ned on input line 30958. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 268 undefined on input line 30973. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 268 undefi ned on input line 30973. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 268 undefined on input line 30977. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 268 undefi ned on input line 30977. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 268 undefined on input line 30977. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 268 undefi ned on input line 30977. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 268 undefined on input line 30977. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 268 undefi ned on input line 30977. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 268 undefined on input line 30977. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 268 undefi ned on input line 30977. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 268 undefi ned on input line 30990. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 268 undefi ned on input line 30990. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 268 undefi ned on input line 30990. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 268 undefi ned on input line 30990. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 268 undefi ned on input line 30990. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 268 undefined on input line 30990. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 268 undefi ned on input line 30990. [268] [269] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31080. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31080. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 270 undefined on input line 31084. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 270 undefi ned on input line 31084. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31085. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31085. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31088. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31088. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31107. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31107. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31110. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31110. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 270 undefined on input line 31116. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 270 undefi ned on input line 31116. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 270 undefined on input line 31119. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 270 undefi ned on input line 31119. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 270 undefined on input line 31122. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 270 undefi ned on input line 31122. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 270 undefined on input line 31125. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 270 undefi ned on input line 31125. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 270 undefine d on input line 31141. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 270 undefined on i nput line 31141. [270] LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 271 undefined on input line 31188. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 271 undefi ned on input line 31188. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 271 undefined on input line 31213. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 271 undefi ned on input line 31213. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 271 undefined on input line 31213. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 271 undefi ned on input line 31213. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 271 undefined on input line 31213. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 271 undefi ned on input line 31213. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 271 undefined on input line 31225. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 271 undefi ned on input line 31225. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 271 undefined on input line 31225. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 271 undefi ned on input line 31225. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 271 undefined on input line 31225. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 271 undefi ned on input line 31225. [271] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 272 undefined on input line 31289. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 272 undefi ned on input line 31289. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 272 undefined on input line 31289. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 272 undefi ned on input line 31289. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 272 undefined on input line 31289. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 272 undefi ned on input line 31289. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 272 undefined on input line 31301. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 272 undefi ned on input line 31301. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 272 undefined on input line 31301. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 272 undefi ned on input line 31301. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 272 undefined on input line 31301. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 272 undefi ned on input line 31301. [272] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 273 undefined on input line 31434. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 273 undefi ned on input line 31434. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 273 undefined on input line 31434. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 273 undefi ned on input line 31434. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 273 undefined on input line 31446. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 273 undefi ned on input line 31446. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 273 undefined on input line 31446. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 273 undefi ned on input line 31446. [273] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 274 undefined on input line 31454. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 274 undefi ned on input line 31454. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 274 undefined on input line 31540. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 274 undefi ned on input line 31540. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 274 undefined on input line 31544. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 274 undefi ned on input line 31544. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 274 undefined on input line 31544. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 274 undefi ned on input line 31544. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 274 undefined on input line 31544. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 274 undefi ned on input line 31544. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 274 undefined on input line 31544. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 274 undefi ned on input line 31544. [274] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 275 undefined on input line 31586. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 275 undefi ned on input line 31586. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 275 undefined on input line 31586. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 275 undefi ned on input line 31586. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 275 undefined on input line 31586. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 275 undefi ned on input line 31586. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 275 undefined on input line 31586. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 275 undefi ned on input line 31586. [275] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 276 undefined on input line 31667. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 276 undefi ned on input line 31667. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 276 undefined on input line 31679. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 276 undefi ned on input line 31679. LaTeX Warning: Hyper reference `reference-manual/file-formats:cpt' on page 276 undefined on input line 31679. LaTeX Warning: Reference `reference-manual/file-formats:cpt' on page 276 undefi ned on input line 31679. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 276 undefined on input line 31679. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 276 undefi ned on input line 31679. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 276 undefined on input line 31683. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 276 undefi ned on input line 31683. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 276 undefined on input line 31683. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 276 undefi ned on input line 31683. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 276 undefined on input line 31683. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 276 undefi ned on input line 31683. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 276 undefined on input line 31683. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 276 undefi ned on input line 31683. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 276 undefined on input line 31721. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 276 undefi ned on input line 31721. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 276 undefined on input line 31721. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 276 undefi ned on input line 31721. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 276 undefined on input line 31721. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 276 undefi ned on input line 31721. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 276 undefined on input line 31721. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 276 undefi ned on input line 31721. [276] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 277 undefined on input line 31807. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 277 undefi ned on input line 31807. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 277 undefined on input line 31809. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 277 undefi ned on input line 31809. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 277 undefined on input line 31810. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 277 undefi ned on input line 31810. [277] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 278 undefined on input line 31855. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 278 undefi ned on input line 31855. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze::doc' on page 278 undefi ned on input line 31931. LaTeX Warning: Reference `onlinehelp/gmx-analyze::doc' on page 278 undefined on input line 31931. [278] [279] [280] LaTeX Warning: Hyper reference `reference-manual/file-formats:dat' on page 281 undefined on input line 32193. LaTeX Warning: Reference `reference-manual/file-formats:dat' on page 281 undefi ned on input line 32193. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 281 undefined on input line 32260. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 281 undefi ned on input line 32260. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 281 undefined on input line 32261. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 281 undefi ned on input line 32261. [281] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 282 undefined on input line 32293. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 282 undefi ned on input line 32293. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 282 undefined on input line 32293. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 282 undefi ned on input line 32293. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 282 undefined on input line 32293. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 282 undefi ned on input line 32293. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 282 undefined on input line 32293. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 282 undefi ned on input line 32293. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 282 undefined on input line 32351. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 282 undefi ned on input line 32351. [282] LaTeX Warning: Hyper reference `onlinehelp/gmx-rms::doc' on page 283 undefined on input line 32420. LaTeX Warning: Reference `onlinehelp/gmx-rms::doc' on page 283 undefined on inp ut line 32420. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdmat::doc' on page 283 undefine d on input line 32421. LaTeX Warning: Reference `onlinehelp/gmx-mdmat::doc' on page 283 undefined on i nput line 32421. [283] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 284 undefined on input line 32512. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 284 undefi ned on input line 32512. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 284 undefined on input line 32512. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 284 undefi ned on input line 32512. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 284 undefined on input line 32512. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 284 undefi ned on input line 32512. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 284 undefined on input line 32512. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 284 undefi ned on input line 32512. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 284 undefined on input line 32560. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 284 undefi ned on input line 32560. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 284 undefined on input line 32564. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 284 undefi ned on input line 32564. [284] LaTeX Warning: Hyper reference `onlinehelp/gmx::doc' on page 285 undefined on i nput line 32605. LaTeX Warning: Reference `onlinehelp/gmx::doc' on page 285 undefined on input l ine 32605. LaTeX Warning: Hyper reference `onlinehelp/selections::doc' on page 285 undefin ed on input line 32672. LaTeX Warning: Reference `onlinehelp/selections::doc' on page 285 undefined on input line 32672. [285] LaTeX Warning: Hyper reference `onlinehelp/gmx::doc' on page 286 undefined on i nput line 32681. LaTeX Warning: Reference `onlinehelp/gmx::doc' on page 286 undefined on input l ine 32681. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig::doc' on page 286 undefin ed on input line 32685. LaTeX Warning: Reference `onlinehelp/gmx-anaeig::doc' on page 286 undefined on input line 32685. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze::doc' on page 286 undefi ned on input line 32689. LaTeX Warning: Reference `onlinehelp/gmx-analyze::doc' on page 286 undefined on input line 32689. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle::doc' on page 286 undefine d on input line 32693. LaTeX Warning: Reference `onlinehelp/gmx-angle::doc' on page 286 undefined on i nput line 32693. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh::doc' on page 286 undefined on input line 32697. LaTeX Warning: Reference `onlinehelp/gmx-awh::doc' on page 286 undefined on inp ut line 32697. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar::doc' on page 286 undefined on input line 32701. LaTeX Warning: Reference `onlinehelp/gmx-bar::doc' on page 286 undefined on inp ut line 32701. LaTeX Warning: Hyper reference `onlinehelp/gmx-bundle::doc' on page 286 undefin ed on input line 32705. LaTeX Warning: Reference `onlinehelp/gmx-bundle::doc' on page 286 undefined on input line 32705. LaTeX Warning: Hyper reference `onlinehelp/gmx-check::doc' on page 286 undefine d on input line 32709. LaTeX Warning: Reference `onlinehelp/gmx-check::doc' on page 286 undefined on i nput line 32709. LaTeX Warning: Hyper reference `onlinehelp/gmx-chi::doc' on page 286 undefined on input line 32713. LaTeX Warning: Reference `onlinehelp/gmx-chi::doc' on page 286 undefined on inp ut line 32713. LaTeX Warning: Hyper reference `onlinehelp/gmx-cluster::doc' on page 286 undefi ned on input line 32717. LaTeX Warning: Reference `onlinehelp/gmx-cluster::doc' on page 286 undefined on input line 32717. LaTeX Warning: Hyper reference `onlinehelp/gmx-clustsize::doc' on page 286 unde fined on input line 32721. LaTeX Warning: Reference `onlinehelp/gmx-clustsize::doc' on page 286 undefined on input line 32721. LaTeX Warning: Hyper reference `onlinehelp/gmx-confrms::doc' on page 286 undefi ned on input line 32725. LaTeX Warning: Reference `onlinehelp/gmx-confrms::doc' on page 286 undefined on input line 32725. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr::doc' on page 286 un defined on input line 32729. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr::doc' on page 286 undefine d on input line 32729. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-trj::doc' on page 286 un defined on input line 32733. LaTeX Warning: Reference `onlinehelp/gmx-convert-trj::doc' on page 286 undefine d on input line 32733. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar::doc' on page 286 undefine d on input line 32737. LaTeX Warning: Reference `onlinehelp/gmx-covar::doc' on page 286 undefined on i nput line 32737. LaTeX Warning: Hyper reference `onlinehelp/gmx-current::doc' on page 286 undefi ned on input line 32741. LaTeX Warning: Reference `onlinehelp/gmx-current::doc' on page 286 undefined on input line 32741. LaTeX Warning: Hyper reference `onlinehelp/gmx-density::doc' on page 286 undefi ned on input line 32745. LaTeX Warning: Reference `onlinehelp/gmx-density::doc' on page 286 undefined on input line 32745. LaTeX Warning: Hyper reference `onlinehelp/gmx-densmap::doc' on page 286 undefi ned on input line 32749. LaTeX Warning: Reference `onlinehelp/gmx-densmap::doc' on page 286 undefined on input line 32749. LaTeX Warning: Hyper reference `onlinehelp/gmx-densorder::doc' on page 286 unde fined on input line 32753. LaTeX Warning: Reference `onlinehelp/gmx-densorder::doc' on page 286 undefined on input line 32753. LaTeX Warning: Hyper reference `onlinehelp/gmx-dielectric::doc' on page 286 und efined on input line 32757. LaTeX Warning: Reference `onlinehelp/gmx-dielectric::doc' on page 286 undefined on input line 32757. LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles::doc' on page 286 undefi ned on input line 32761. LaTeX Warning: Reference `onlinehelp/gmx-dipoles::doc' on page 286 undefined on input line 32761. LaTeX Warning: Hyper reference `onlinehelp/gmx-disre::doc' on page 286 undefine d on input line 32765. LaTeX Warning: Reference `onlinehelp/gmx-disre::doc' on page 286 undefined on i nput line 32765. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance::doc' on page 286 undef ined on input line 32769. LaTeX Warning: Reference `onlinehelp/gmx-distance::doc' on page 286 undefined o n input line 32769. LaTeX Warning: Hyper reference `onlinehelp/gmx-dos::doc' on page 286 undefined on input line 32773. LaTeX Warning: Reference `onlinehelp/gmx-dos::doc' on page 286 undefined on inp ut line 32773. LaTeX Warning: Hyper reference `onlinehelp/gmx-dssp::doc' on page 286 undefined on input line 32777. LaTeX Warning: Reference `onlinehelp/gmx-dssp::doc' on page 286 undefined on in put line 32777. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump::doc' on page 286 undefined on input line 32781. LaTeX Warning: Reference `onlinehelp/gmx-dump::doc' on page 286 undefined on in put line 32781. LaTeX Warning: Hyper reference `onlinehelp/gmx-dyecoupl::doc' on page 286 undef ined on input line 32785. LaTeX Warning: Reference `onlinehelp/gmx-dyecoupl::doc' on page 286 undefined o n input line 32785. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 286 undef ined on input line 32789. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 286 undefined o n input line 32789. LaTeX Warning: Hyper reference `onlinehelp/gmx-eneconv::doc' on page 286 undefi ned on input line 32793. LaTeX Warning: Reference `onlinehelp/gmx-eneconv::doc' on page 286 undefined on input line 32793. LaTeX Warning: Hyper reference `onlinehelp/gmx-enemat::doc' on page 286 undefin ed on input line 32797. LaTeX Warning: Reference `onlinehelp/gmx-enemat::doc' on page 286 undefined on input line 32797. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy::doc' on page 286 undefin ed on input line 32801. LaTeX Warning: Reference `onlinehelp/gmx-energy::doc' on page 286 undefined on input line 32801. LaTeX Warning: Hyper reference `onlinehelp/gmx-extract-cluster::doc' on page 28 6 undefined on input line 32805. LaTeX Warning: Reference `onlinehelp/gmx-extract-cluster::doc' on page 286 unde fined on input line 32805. LaTeX Warning: Hyper reference `onlinehelp/gmx-filter::doc' on page 286 undefin ed on input line 32809. LaTeX Warning: Reference `onlinehelp/gmx-filter::doc' on page 286 undefined on input line 32809. LaTeX Warning: Hyper reference `onlinehelp/gmx-freevolume::doc' on page 286 und efined on input line 32813. LaTeX Warning: Reference `onlinehelp/gmx-freevolume::doc' on page 286 undefined on input line 32813. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle::doc' on page 286 undefin ed on input line 32817. LaTeX Warning: Reference `onlinehelp/gmx-gangle::doc' on page 286 undefined on input line 32817. LaTeX Warning: Hyper reference `onlinehelp/gmx-genconf::doc' on page 286 undefi ned on input line 32821. LaTeX Warning: Reference `onlinehelp/gmx-genconf::doc' on page 286 undefined on input line 32821. LaTeX Warning: Hyper reference `onlinehelp/gmx-genion::doc' on page 286 undefin ed on input line 32825. LaTeX Warning: Reference `onlinehelp/gmx-genion::doc' on page 286 undefined on input line 32825. LaTeX Warning: Hyper reference `onlinehelp/gmx-genrestr::doc' on page 286 undef ined on input line 32829. LaTeX Warning: Reference `onlinehelp/gmx-genrestr::doc' on page 286 undefined o n input line 32829. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp::doc' on page 286 undefin ed on input line 32833. LaTeX Warning: Reference `onlinehelp/gmx-grompp::doc' on page 286 undefined on input line 32833. [286] LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate::doc' on page 287 undefin ed on input line 32837. LaTeX Warning: Reference `onlinehelp/gmx-gyrate::doc' on page 287 undefined on input line 32837. LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate-legacy::doc' on page 287 undefined on input line 32841. LaTeX Warning: Reference `onlinehelp/gmx-gyrate-legacy::doc' on page 287 undefi ned on input line 32841. LaTeX Warning: Hyper reference `onlinehelp/gmx-h2order::doc' on page 287 undefi ned on input line 32845. LaTeX Warning: Reference `onlinehelp/gmx-h2order::doc' on page 287 undefined on input line 32845. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond::doc' on page 287 undefine d on input line 32849. LaTeX Warning: Reference `onlinehelp/gmx-hbond::doc' on page 287 undefined on i nput line 32849. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond-legacy::doc' on page 287 u ndefined on input line 32853. LaTeX Warning: Reference `onlinehelp/gmx-hbond-legacy::doc' on page 287 undefin ed on input line 32853. LaTeX Warning: Hyper reference `onlinehelp/gmx-helix::doc' on page 287 undefine d on input line 32857. LaTeX Warning: Reference `onlinehelp/gmx-helix::doc' on page 287 undefined on i nput line 32857. LaTeX Warning: Hyper reference `onlinehelp/gmx-helixorient::doc' on page 287 un defined on input line 32861. LaTeX Warning: Reference `onlinehelp/gmx-helixorient::doc' on page 287 undefine d on input line 32861. LaTeX Warning: Hyper reference `onlinehelp/gmx-help::doc' on page 287 undefined on input line 32865. LaTeX Warning: Reference `onlinehelp/gmx-help::doc' on page 287 undefined on in put line 32865. LaTeX Warning: Hyper reference `onlinehelp/gmx-hydorder::doc' on page 287 undef ined on input line 32869. LaTeX Warning: Reference `onlinehelp/gmx-hydorder::doc' on page 287 undefined o n input line 32869. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules::doc' on page 2 87 undefined on input line 32873. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules::doc' on page 287 und efined on input line 32873. LaTeX Warning: Hyper reference `onlinehelp/gmx-lie::doc' on page 287 undefined on input line 32877. LaTeX Warning: Reference `onlinehelp/gmx-lie::doc' on page 287 undefined on inp ut line 32877. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_edi::doc' on page 287 undef ined on input line 32881. LaTeX Warning: Reference `onlinehelp/gmx-make_edi::doc' on page 287 undefined o n input line 32881. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx::doc' on page 287 undef ined on input line 32885. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx::doc' on page 287 undefined o n input line 32885. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdmat::doc' on page 287 undefine d on input line 32889. LaTeX Warning: Reference `onlinehelp/gmx-mdmat::doc' on page 287 undefined on i nput line 32889. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 287 undefine d on input line 32893. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 287 undefined on i nput line 32893. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist::doc' on page 287 undefi ned on input line 32897. LaTeX Warning: Reference `onlinehelp/gmx-mindist::doc' on page 287 undefined on input line 32897. LaTeX Warning: Hyper reference `onlinehelp/gmx-mk_angndx::doc' on page 287 unde fined on input line 32901. LaTeX Warning: Reference `onlinehelp/gmx-mk_angndx::doc' on page 287 undefined on input line 32901. LaTeX Warning: Hyper reference `onlinehelp/gmx-msd::doc' on page 287 undefined on input line 32905. LaTeX Warning: Reference `onlinehelp/gmx-msd::doc' on page 287 undefined on inp ut line 32905. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig::doc' on page 287 undefine d on input line 32909. LaTeX Warning: Reference `onlinehelp/gmx-nmeig::doc' on page 287 undefined on i nput line 32909. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmens::doc' on page 287 undefine d on input line 32913. LaTeX Warning: Reference `onlinehelp/gmx-nmens::doc' on page 287 undefined on i nput line 32913. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmr::doc' on page 287 undefined on input line 32917. LaTeX Warning: Reference `onlinehelp/gmx-nmr::doc' on page 287 undefined on inp ut line 32917. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmtraj::doc' on page 287 undefin ed on input line 32921. LaTeX Warning: Reference `onlinehelp/gmx-nmtraj::doc' on page 287 undefined on input line 32921. LaTeX Warning: Hyper reference `onlinehelp/gmx-nonbonded-benchmark::doc' on pag e 287 undefined on input line 32925. LaTeX Warning: Reference `onlinehelp/gmx-nonbonded-benchmark::doc' on page 287 undefined on input line 32925. LaTeX Warning: Hyper reference `onlinehelp/gmx-order::doc' on page 287 undefine d on input line 32929. LaTeX Warning: Reference `onlinehelp/gmx-order::doc' on page 287 undefined on i nput line 32929. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist::doc' on page 287 undef ined on input line 32933. LaTeX Warning: Reference `onlinehelp/gmx-pairdist::doc' on page 287 undefined o n input line 32933. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx::doc' on page 287 undefi ned on input line 32937. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx::doc' on page 287 undefined on input line 32937. LaTeX Warning: Hyper reference `onlinehelp/gmx-pme_error::doc' on page 287 unde fined on input line 32941. LaTeX Warning: Reference `onlinehelp/gmx-pme_error::doc' on page 287 undefined on input line 32941. LaTeX Warning: Hyper reference `onlinehelp/gmx-polystat::doc' on page 287 undef ined on input line 32945. LaTeX Warning: Reference `onlinehelp/gmx-polystat::doc' on page 287 undefined o n input line 32945. LaTeX Warning: Hyper reference `onlinehelp/gmx-potential::doc' on page 287 unde fined on input line 32949. LaTeX Warning: Reference `onlinehelp/gmx-potential::doc' on page 287 undefined on input line 32949. LaTeX Warning: Hyper reference `onlinehelp/gmx-principal::doc' on page 287 unde fined on input line 32953. LaTeX Warning: Reference `onlinehelp/gmx-principal::doc' on page 287 undefined on input line 32953. LaTeX Warning: Hyper reference `onlinehelp/gmx-rama::doc' on page 287 undefined on input line 32957. LaTeX Warning: Reference `onlinehelp/gmx-rama::doc' on page 287 undefined on in put line 32957. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf::doc' on page 287 undefined on input line 32961. LaTeX Warning: Reference `onlinehelp/gmx-rdf::doc' on page 287 undefined on inp ut line 32961. LaTeX Warning: Hyper reference `onlinehelp/gmx-report-methods::doc' on page 287 undefined on input line 32965. LaTeX Warning: Reference `onlinehelp/gmx-report-methods::doc' on page 287 undef ined on input line 32965. LaTeX Warning: Hyper reference `onlinehelp/gmx-rms::doc' on page 287 undefined on input line 32969. LaTeX Warning: Reference `onlinehelp/gmx-rms::doc' on page 287 undefined on inp ut line 32969. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsdist::doc' on page 287 undefi ned on input line 32973. LaTeX Warning: Reference `onlinehelp/gmx-rmsdist::doc' on page 287 undefined on input line 32973. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsf::doc' on page 287 undefined on input line 32977. LaTeX Warning: Reference `onlinehelp/gmx-rmsf::doc' on page 287 undefined on in put line 32977. LaTeX Warning: Hyper reference `onlinehelp/gmx-rotacf::doc' on page 287 undefin ed on input line 32981. LaTeX Warning: Reference `onlinehelp/gmx-rotacf::doc' on page 287 undefined on input line 32981. LaTeX Warning: Hyper reference `onlinehelp/gmx-rotmat::doc' on page 287 undefin ed on input line 32985. LaTeX Warning: Reference `onlinehelp/gmx-rotmat::doc' on page 287 undefined on input line 32985. [287] LaTeX Warning: Hyper reference `onlinehelp/gmx-saltbr::doc' on page 288 undefin ed on input line 32989. LaTeX Warning: Reference `onlinehelp/gmx-saltbr::doc' on page 288 undefined on input line 32989. LaTeX Warning: Hyper reference `onlinehelp/gmx-sans-legacy::doc' on page 288 un defined on input line 32993. LaTeX Warning: Reference `onlinehelp/gmx-sans-legacy::doc' on page 288 undefine d on input line 32993. LaTeX Warning: Hyper reference `onlinehelp/gmx-sasa::doc' on page 288 undefined on input line 32997. LaTeX Warning: Reference `onlinehelp/gmx-sasa::doc' on page 288 undefined on in put line 32997. LaTeX Warning: Hyper reference `onlinehelp/gmx-saxs-legacy::doc' on page 288 un defined on input line 33001. LaTeX Warning: Reference `onlinehelp/gmx-saxs-legacy::doc' on page 288 undefine d on input line 33001. LaTeX Warning: Hyper reference `onlinehelp/gmx-scattering::doc' on page 288 und efined on input line 33005. LaTeX Warning: Reference `onlinehelp/gmx-scattering::doc' on page 288 undefined on input line 33005. LaTeX Warning: Hyper reference `onlinehelp/gmx-select::doc' on page 288 undefin ed on input line 33009. LaTeX Warning: Reference `onlinehelp/gmx-select::doc' on page 288 undefined on input line 33009. LaTeX Warning: Hyper reference `onlinehelp/gmx-sham::doc' on page 288 undefined on input line 33013. LaTeX Warning: Reference `onlinehelp/gmx-sham::doc' on page 288 undefined on in put line 33013. LaTeX Warning: Hyper reference `onlinehelp/gmx-sigeps::doc' on page 288 undefin ed on input line 33017. LaTeX Warning: Reference `onlinehelp/gmx-sigeps::doc' on page 288 undefined on input line 33017. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate::doc' on page 288 undefi ned on input line 33021. LaTeX Warning: Reference `onlinehelp/gmx-solvate::doc' on page 288 undefined on input line 33021. LaTeX Warning: Hyper reference `onlinehelp/gmx-sorient::doc' on page 288 undefi ned on input line 33025. LaTeX Warning: Reference `onlinehelp/gmx-sorient::doc' on page 288 undefined on input line 33025. LaTeX Warning: Hyper reference `onlinehelp/gmx-spatial::doc' on page 288 undefi ned on input line 33029. LaTeX Warning: Reference `onlinehelp/gmx-spatial::doc' on page 288 undefined on input line 33029. LaTeX Warning: Hyper reference `onlinehelp/gmx-spol::doc' on page 288 undefined on input line 33033. LaTeX Warning: Reference `onlinehelp/gmx-spol::doc' on page 288 undefined on in put line 33033. LaTeX Warning: Hyper reference `onlinehelp/gmx-tcaf::doc' on page 288 undefined on input line 33037. LaTeX Warning: Reference `onlinehelp/gmx-tcaf::doc' on page 288 undefined on in put line 33037. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj::doc' on page 288 undefined on input line 33041. LaTeX Warning: Reference `onlinehelp/gmx-traj::doc' on page 288 undefined on in put line 33041. LaTeX Warning: Hyper reference `onlinehelp/gmx-trajectory::doc' on page 288 und efined on input line 33045. LaTeX Warning: Reference `onlinehelp/gmx-trajectory::doc' on page 288 undefined on input line 33045. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjcat::doc' on page 288 undefin ed on input line 33049. LaTeX Warning: Reference `onlinehelp/gmx-trjcat::doc' on page 288 undefined on input line 33049. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 288 undefi ned on input line 33053. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 288 undefined on input line 33053. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjorder::doc' on page 288 undef ined on input line 33057. LaTeX Warning: Reference `onlinehelp/gmx-trjorder::doc' on page 288 undefined o n input line 33057. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme::doc' on page 288 undef ined on input line 33061. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme::doc' on page 288 undefined o n input line 33061. LaTeX Warning: Hyper reference `onlinehelp/gmx-vanhove::doc' on page 288 undefi ned on input line 33065. LaTeX Warning: Reference `onlinehelp/gmx-vanhove::doc' on page 288 undefined on input line 33065. LaTeX Warning: Hyper reference `onlinehelp/gmx-velacc::doc' on page 288 undefin ed on input line 33069. LaTeX Warning: Reference `onlinehelp/gmx-velacc::doc' on page 288 undefined on input line 33069. LaTeX Warning: Hyper reference `onlinehelp/gmx-wham::doc' on page 288 undefined on input line 33073. LaTeX Warning: Reference `onlinehelp/gmx-wham::doc' on page 288 undefined on in put line 33073. LaTeX Warning: Hyper reference `onlinehelp/gmx-wheel::doc' on page 288 undefine d on input line 33077. LaTeX Warning: Reference `onlinehelp/gmx-wheel::doc' on page 288 undefined on i nput line 33077. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top::doc' on page 288 undefine d on input line 33081. LaTeX Warning: Reference `onlinehelp/gmx-x2top::doc' on page 288 undefined on i nput line 33081. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps::doc' on page 288 undefin ed on input line 33085. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps::doc' on page 288 undefined on input line 33085. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle::doc' on page 288 undefin ed on input line 33096. LaTeX Warning: Reference `onlinehelp/gmx-gangle::doc' on page 288 undefined on input line 33096. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-trj::doc' on page 288 un defined on input line 33100. LaTeX Warning: Reference `onlinehelp/gmx-convert-trj::doc' on page 288 undefine d on input line 33100. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance::doc' on page 288 undef ined on input line 33104. LaTeX Warning: Reference `onlinehelp/gmx-distance::doc' on page 288 undefined o n input line 33104. LaTeX Warning: Hyper reference `onlinehelp/gmx-dssp::doc' on page 288 undefined on input line 33108. LaTeX Warning: Reference `onlinehelp/gmx-dssp::doc' on page 288 undefined on in put line 33108. LaTeX Warning: Hyper reference `onlinehelp/gmx-extract-cluster::doc' on page 28 8 undefined on input line 33112. LaTeX Warning: Reference `onlinehelp/gmx-extract-cluster::doc' on page 288 unde fined on input line 33112. LaTeX Warning: Hyper reference `onlinehelp/gmx-freevolume::doc' on page 288 und efined on input line 33116. LaTeX Warning: Reference `onlinehelp/gmx-freevolume::doc' on page 288 undefined on input line 33116. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond::doc' on page 288 undefine d on input line 33120. LaTeX Warning: Reference `onlinehelp/gmx-hbond::doc' on page 288 undefined on i nput line 33120. [288] LaTeX Warning: Hyper reference `onlinehelp/gmx-msd::doc' on page 289 undefined on input line 33124. LaTeX Warning: Reference `onlinehelp/gmx-msd::doc' on page 289 undefined on inp ut line 33124. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist::doc' on page 289 undef ined on input line 33128. LaTeX Warning: Reference `onlinehelp/gmx-pairdist::doc' on page 289 undefined o n input line 33128. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf::doc' on page 289 undefined on input line 33132. LaTeX Warning: Reference `onlinehelp/gmx-rdf::doc' on page 289 undefined on inp ut line 33132. LaTeX Warning: Hyper reference `onlinehelp/gmx-sasa::doc' on page 289 undefined on input line 33136. LaTeX Warning: Reference `onlinehelp/gmx-sasa::doc' on page 289 undefined on in put line 33136. LaTeX Warning: Hyper reference `onlinehelp/gmx-scattering::doc' on page 289 und efined on input line 33140. LaTeX Warning: Reference `onlinehelp/gmx-scattering::doc' on page 289 undefined on input line 33140. LaTeX Warning: Hyper reference `onlinehelp/gmx-select::doc' on page 289 undefin ed on input line 33144. LaTeX Warning: Reference `onlinehelp/gmx-select::doc' on page 289 undefined on input line 33144. LaTeX Warning: Hyper reference `onlinehelp/gmx-trajectory::doc' on page 289 und efined on input line 33148. LaTeX Warning: Reference `onlinehelp/gmx-trajectory::doc' on page 289 undefined on input line 33148. LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate::doc' on page 289 undefin ed on input line 33152. LaTeX Warning: Reference `onlinehelp/gmx-gyrate::doc' on page 289 undefined on input line 33152. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 289 undef ined on input line 33161. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 289 undefined o n input line 33161. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top::doc' on page 289 undefine d on input line 33165. LaTeX Warning: Reference `onlinehelp/gmx-x2top::doc' on page 289 undefined on i nput line 33165. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate::doc' on page 289 undefi ned on input line 33169. LaTeX Warning: Reference `onlinehelp/gmx-solvate::doc' on page 289 undefined on input line 33169. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules::doc' on page 2 89 undefined on input line 33173. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules::doc' on page 289 und efined on input line 33173. LaTeX Warning: Hyper reference `onlinehelp/gmx-genconf::doc' on page 289 undefi ned on input line 33177. LaTeX Warning: Reference `onlinehelp/gmx-genconf::doc' on page 289 undefined on input line 33177. LaTeX Warning: Hyper reference `onlinehelp/gmx-genion::doc' on page 289 undefin ed on input line 33181. LaTeX Warning: Reference `onlinehelp/gmx-genion::doc' on page 289 undefined on input line 33181. LaTeX Warning: Hyper reference `onlinehelp/gmx-genrestr::doc' on page 289 undef ined on input line 33185. LaTeX Warning: Reference `onlinehelp/gmx-genrestr::doc' on page 289 undefined o n input line 33185. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx::doc' on page 289 undefi ned on input line 33189. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx::doc' on page 289 undefined on input line 33189. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp::doc' on page 289 undefin ed on input line 33198. LaTeX Warning: Reference `onlinehelp/gmx-grompp::doc' on page 289 undefined on input line 33198. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 289 undefine d on input line 33202. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 289 undefined on i nput line 33202. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr::doc' on page 289 un defined on input line 33206. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr::doc' on page 289 undefine d on input line 33206. [289] LaTeX Warning: Hyper reference `onlinehelp/gmx-nmtraj::doc' on page 290 undefin ed on input line 33215. LaTeX Warning: Reference `onlinehelp/gmx-nmtraj::doc' on page 290 undefined on input line 33215. LaTeX Warning: Hyper reference `onlinehelp/gmx-enemat::doc' on page 290 undefin ed on input line 33224. LaTeX Warning: Reference `onlinehelp/gmx-enemat::doc' on page 290 undefined on input line 33224. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy::doc' on page 290 undefin ed on input line 33228. LaTeX Warning: Reference `onlinehelp/gmx-energy::doc' on page 290 undefined on input line 33228. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 290 undefine d on input line 33232. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 290 undefined on i nput line 33232. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf::doc' on page 290 undef ined on input line 33241. LaTeX Warning: Reference `onlinehelp/gmx-editconf::doc' on page 290 undefined o n input line 33241. LaTeX Warning: Hyper reference `onlinehelp/gmx-eneconv::doc' on page 290 undefi ned on input line 33245. LaTeX Warning: Reference `onlinehelp/gmx-eneconv::doc' on page 290 undefined on input line 33245. LaTeX Warning: Hyper reference `onlinehelp/gmx-sigeps::doc' on page 290 undefin ed on input line 33249. LaTeX Warning: Reference `onlinehelp/gmx-sigeps::doc' on page 290 undefined on input line 33249. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjcat::doc' on page 290 undefin ed on input line 33253. LaTeX Warning: Reference `onlinehelp/gmx-trjcat::doc' on page 290 undefined on input line 33253. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv::doc' on page 290 undefi ned on input line 33257. LaTeX Warning: Reference `onlinehelp/gmx-trjconv::doc' on page 290 undefined on input line 33257. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps::doc' on page 290 undefin ed on input line 33261. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps::doc' on page 290 undefined on input line 33261. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze::doc' on page 290 undefi ned on input line 33270. LaTeX Warning: Reference `onlinehelp/gmx-analyze::doc' on page 290 undefined on input line 33270. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh::doc' on page 290 undefined on input line 33274. LaTeX Warning: Reference `onlinehelp/gmx-awh::doc' on page 290 undefined on inp ut line 33274. LaTeX Warning: Hyper reference `onlinehelp/gmx-filter::doc' on page 290 undefin ed on input line 33278. LaTeX Warning: Reference `onlinehelp/gmx-filter::doc' on page 290 undefined on input line 33278. LaTeX Warning: Hyper reference `onlinehelp/gmx-lie::doc' on page 290 undefined on input line 33282. LaTeX Warning: Reference `onlinehelp/gmx-lie::doc' on page 290 undefined on inp ut line 33282. LaTeX Warning: Hyper reference `onlinehelp/gmx-pme_error::doc' on page 290 unde fined on input line 33286. LaTeX Warning: Reference `onlinehelp/gmx-pme_error::doc' on page 290 undefined on input line 33286. LaTeX Warning: Hyper reference `onlinehelp/gmx-sham::doc' on page 290 undefined on input line 33290. LaTeX Warning: Reference `onlinehelp/gmx-sham::doc' on page 290 undefined on in put line 33290. LaTeX Warning: Hyper reference `onlinehelp/gmx-spatial::doc' on page 290 undefi ned on input line 33294. LaTeX Warning: Reference `onlinehelp/gmx-spatial::doc' on page 290 undefined on input line 33294. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj::doc' on page 290 undefined on input line 33298. LaTeX Warning: Reference `onlinehelp/gmx-traj::doc' on page 290 undefined on in put line 33298. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme::doc' on page 290 undef ined on input line 33302. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme::doc' on page 290 undefined o n input line 33302. LaTeX Warning: Hyper reference `onlinehelp/gmx-wham::doc' on page 290 undefined on input line 33306. LaTeX Warning: Reference `onlinehelp/gmx-wham::doc' on page 290 undefined on in put line 33306. LaTeX Warning: Hyper reference `onlinehelp/gmx-check::doc' on page 290 undefine d on input line 33310. LaTeX Warning: Reference `onlinehelp/gmx-check::doc' on page 290 undefined on i nput line 33310. [290] LaTeX Warning: Hyper reference `onlinehelp/gmx-dump::doc' on page 291 undefined on input line 33314. LaTeX Warning: Reference `onlinehelp/gmx-dump::doc' on page 291 undefined on in put line 33314. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx::doc' on page 291 undef ined on input line 33318. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx::doc' on page 291 undefined o n input line 33318. LaTeX Warning: Hyper reference `onlinehelp/gmx-mk_angndx::doc' on page 291 unde fined on input line 33322. LaTeX Warning: Reference `onlinehelp/gmx-mk_angndx::doc' on page 291 undefined on input line 33322. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjorder::doc' on page 291 undef ined on input line 33326. LaTeX Warning: Reference `onlinehelp/gmx-trjorder::doc' on page 291 undefined o n input line 33326. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps::doc' on page 291 undefin ed on input line 33330. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps::doc' on page 291 undefined on input line 33330. LaTeX Warning: Hyper reference `onlinehelp/gmx-report-methods::doc' on page 291 undefined on input line 33334. LaTeX Warning: Reference `onlinehelp/gmx-report-methods::doc' on page 291 undef ined on input line 33334. LaTeX Warning: Hyper reference `onlinehelp/gmx-cluster::doc' on page 291 undefi ned on input line 33343. LaTeX Warning: Reference `onlinehelp/gmx-cluster::doc' on page 291 undefined on input line 33343. LaTeX Warning: Hyper reference `onlinehelp/gmx-confrms::doc' on page 291 undefi ned on input line 33347. LaTeX Warning: Reference `onlinehelp/gmx-confrms::doc' on page 291 undefined on input line 33347. LaTeX Warning: Hyper reference `onlinehelp/gmx-rms::doc' on page 291 undefined on input line 33351. LaTeX Warning: Reference `onlinehelp/gmx-rms::doc' on page 291 undefined on inp ut line 33351. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsf::doc' on page 291 undefined on input line 33355. LaTeX Warning: Reference `onlinehelp/gmx-rmsf::doc' on page 291 undefined on in put line 33355. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist::doc' on page 291 undefi ned on input line 33364. LaTeX Warning: Reference `onlinehelp/gmx-mindist::doc' on page 291 undefined on input line 33364. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdmat::doc' on page 291 undefine d on input line 33368. LaTeX Warning: Reference `onlinehelp/gmx-mdmat::doc' on page 291 undefined on i nput line 33368. LaTeX Warning: Hyper reference `onlinehelp/gmx-polystat::doc' on page 291 undef ined on input line 33372. LaTeX Warning: Reference `onlinehelp/gmx-polystat::doc' on page 291 undefined o n input line 33372. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsdist::doc' on page 291 undefi ned on input line 33376. LaTeX Warning: Reference `onlinehelp/gmx-rmsdist::doc' on page 291 undefined on input line 33376. LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate-legacy::doc' on page 291 undefined on input line 33385. LaTeX Warning: Reference `onlinehelp/gmx-gyrate-legacy::doc' on page 291 undefi ned on input line 33385. LaTeX Warning: Hyper reference `onlinehelp/gmx-polystat::doc' on page 291 undef ined on input line 33389. LaTeX Warning: Reference `onlinehelp/gmx-polystat::doc' on page 291 undefined o n input line 33389. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf::doc' on page 291 undefined on input line 33393. LaTeX Warning: Reference `onlinehelp/gmx-rdf::doc' on page 291 undefined on inp ut line 33393. LaTeX Warning: Hyper reference `onlinehelp/gmx-rotacf::doc' on page 291 undefin ed on input line 33397. LaTeX Warning: Reference `onlinehelp/gmx-rotacf::doc' on page 291 undefined on input line 33397. LaTeX Warning: Hyper reference `onlinehelp/gmx-rotmat::doc' on page 291 undefin ed on input line 33401. LaTeX Warning: Reference `onlinehelp/gmx-rotmat::doc' on page 291 undefined on input line 33401. LaTeX Warning: Hyper reference `onlinehelp/gmx-sans-legacy::doc' on page 291 un defined on input line 33405. LaTeX Warning: Reference `onlinehelp/gmx-sans-legacy::doc' on page 291 undefine d on input line 33405. LaTeX Warning: Hyper reference `onlinehelp/gmx-saxs-legacy::doc' on page 291 un defined on input line 33409. LaTeX Warning: Reference `onlinehelp/gmx-saxs-legacy::doc' on page 291 undefine d on input line 33409. [291] LaTeX Warning: Hyper reference `onlinehelp/gmx-traj::doc' on page 292 undefined on input line 33413. LaTeX Warning: Reference `onlinehelp/gmx-traj::doc' on page 292 undefined on in put line 33413. LaTeX Warning: Hyper reference `onlinehelp/gmx-vanhove::doc' on page 292 undefi ned on input line 33417. LaTeX Warning: Reference `onlinehelp/gmx-vanhove::doc' on page 292 undefined on input line 33417. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle::doc' on page 292 undefine d on input line 33426. LaTeX Warning: Reference `onlinehelp/gmx-angle::doc' on page 292 undefined on i nput line 33426. LaTeX Warning: Hyper reference `onlinehelp/gmx-mk_angndx::doc' on page 292 unde fined on input line 33430. LaTeX Warning: Reference `onlinehelp/gmx-mk_angndx::doc' on page 292 undefined on input line 33430. LaTeX Warning: Hyper reference `onlinehelp/gmx-bundle::doc' on page 292 undefin ed on input line 33439. LaTeX Warning: Reference `onlinehelp/gmx-bundle::doc' on page 292 undefined on input line 33439. LaTeX Warning: Hyper reference `onlinehelp/gmx-clustsize::doc' on page 292 unde fined on input line 33443. LaTeX Warning: Reference `onlinehelp/gmx-clustsize::doc' on page 292 undefined on input line 33443. LaTeX Warning: Hyper reference `onlinehelp/gmx-disre::doc' on page 292 undefine d on input line 33447. LaTeX Warning: Reference `onlinehelp/gmx-disre::doc' on page 292 undefined on i nput line 33447. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond-legacy::doc' on page 292 u ndefined on input line 33451. LaTeX Warning: Reference `onlinehelp/gmx-hbond-legacy::doc' on page 292 undefin ed on input line 33451. LaTeX Warning: Hyper reference `onlinehelp/gmx-order::doc' on page 292 undefine d on input line 33455. LaTeX Warning: Reference `onlinehelp/gmx-order::doc' on page 292 undefined on i nput line 33455. LaTeX Warning: Hyper reference `onlinehelp/gmx-principal::doc' on page 292 unde fined on input line 33459. LaTeX Warning: Reference `onlinehelp/gmx-principal::doc' on page 292 undefined on input line 33459. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf::doc' on page 292 undefined on input line 33463. LaTeX Warning: Reference `onlinehelp/gmx-rdf::doc' on page 292 undefined on inp ut line 33463. LaTeX Warning: Hyper reference `onlinehelp/gmx-saltbr::doc' on page 292 undefin ed on input line 33467. LaTeX Warning: Reference `onlinehelp/gmx-saltbr::doc' on page 292 undefined on input line 33467. LaTeX Warning: Hyper reference `onlinehelp/gmx-sorient::doc' on page 292 undefi ned on input line 33471. LaTeX Warning: Reference `onlinehelp/gmx-sorient::doc' on page 292 undefined on input line 33471. LaTeX Warning: Hyper reference `onlinehelp/gmx-spol::doc' on page 292 undefined on input line 33475. LaTeX Warning: Reference `onlinehelp/gmx-spol::doc' on page 292 undefined on in put line 33475. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar::doc' on page 292 undefined on input line 33484. LaTeX Warning: Reference `onlinehelp/gmx-bar::doc' on page 292 undefined on inp ut line 33484. LaTeX Warning: Hyper reference `onlinehelp/gmx-current::doc' on page 292 undefi ned on input line 33488. LaTeX Warning: Reference `onlinehelp/gmx-current::doc' on page 292 undefined on input line 33488. LaTeX Warning: Hyper reference `onlinehelp/gmx-dos::doc' on page 292 undefined on input line 33492. LaTeX Warning: Reference `onlinehelp/gmx-dos::doc' on page 292 undefined on inp ut line 33492. LaTeX Warning: Hyper reference `onlinehelp/gmx-dyecoupl::doc' on page 292 undef ined on input line 33496. LaTeX Warning: Reference `onlinehelp/gmx-dyecoupl::doc' on page 292 undefined o n input line 33496. LaTeX Warning: Hyper reference `onlinehelp/gmx-principal::doc' on page 292 unde fined on input line 33500. LaTeX Warning: Reference `onlinehelp/gmx-principal::doc' on page 292 undefined on input line 33500. LaTeX Warning: Hyper reference `onlinehelp/gmx-tcaf::doc' on page 292 undefined on input line 33504. LaTeX Warning: Reference `onlinehelp/gmx-tcaf::doc' on page 292 undefined on in put line 33504. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj::doc' on page 292 undefined on input line 33508. LaTeX Warning: Reference `onlinehelp/gmx-traj::doc' on page 292 undefined on in put line 33508. [292] LaTeX Warning: Hyper reference `onlinehelp/gmx-vanhove::doc' on page 293 undefi ned on input line 33512. LaTeX Warning: Reference `onlinehelp/gmx-vanhove::doc' on page 293 undefined on input line 33512. LaTeX Warning: Hyper reference `onlinehelp/gmx-velacc::doc' on page 293 undefin ed on input line 33516. LaTeX Warning: Reference `onlinehelp/gmx-velacc::doc' on page 293 undefined on input line 33516. LaTeX Warning: Hyper reference `onlinehelp/gmx-current::doc' on page 293 undefi ned on input line 33525. LaTeX Warning: Reference `onlinehelp/gmx-current::doc' on page 293 undefined on input line 33525. LaTeX Warning: Hyper reference `onlinehelp/gmx-dielectric::doc' on page 293 und efined on input line 33529. LaTeX Warning: Reference `onlinehelp/gmx-dielectric::doc' on page 293 undefined on input line 33529. LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles::doc' on page 293 undefi ned on input line 33533. LaTeX Warning: Reference `onlinehelp/gmx-dipoles::doc' on page 293 undefined on input line 33533. LaTeX Warning: Hyper reference `onlinehelp/gmx-potential::doc' on page 293 unde fined on input line 33537. LaTeX Warning: Reference `onlinehelp/gmx-potential::doc' on page 293 undefined on input line 33537. LaTeX Warning: Hyper reference `onlinehelp/gmx-spol::doc' on page 293 undefined on input line 33541. LaTeX Warning: Reference `onlinehelp/gmx-spol::doc' on page 293 undefined on in put line 33541. LaTeX Warning: Hyper reference `onlinehelp/gmx-genion::doc' on page 293 undefin ed on input line 33545. LaTeX Warning: Reference `onlinehelp/gmx-genion::doc' on page 293 undefined on input line 33545. LaTeX Warning: Hyper reference `onlinehelp/gmx-chi::doc' on page 293 undefined on input line 33554. LaTeX Warning: Reference `onlinehelp/gmx-chi::doc' on page 293 undefined on inp ut line 33554. LaTeX Warning: Hyper reference `onlinehelp/gmx-helix::doc' on page 293 undefine d on input line 33558. LaTeX Warning: Reference `onlinehelp/gmx-helix::doc' on page 293 undefined on i nput line 33558. LaTeX Warning: Hyper reference `onlinehelp/gmx-helixorient::doc' on page 293 un defined on input line 33562. LaTeX Warning: Reference `onlinehelp/gmx-helixorient::doc' on page 293 undefine d on input line 33562. LaTeX Warning: Hyper reference `onlinehelp/gmx-rama::doc' on page 293 undefined on input line 33566. LaTeX Warning: Reference `onlinehelp/gmx-rama::doc' on page 293 undefined on in put line 33566. LaTeX Warning: Hyper reference `onlinehelp/gmx-wheel::doc' on page 293 undefine d on input line 33570. LaTeX Warning: Reference `onlinehelp/gmx-wheel::doc' on page 293 undefined on i nput line 33570. LaTeX Warning: Hyper reference `onlinehelp/gmx-bundle::doc' on page 293 undefin ed on input line 33579. LaTeX Warning: Reference `onlinehelp/gmx-bundle::doc' on page 293 undefined on input line 33579. LaTeX Warning: Hyper reference `onlinehelp/gmx-density::doc' on page 293 undefi ned on input line 33583. LaTeX Warning: Reference `onlinehelp/gmx-density::doc' on page 293 undefined on input line 33583. LaTeX Warning: Hyper reference `onlinehelp/gmx-densmap::doc' on page 293 undefi ned on input line 33587. LaTeX Warning: Reference `onlinehelp/gmx-densmap::doc' on page 293 undefined on input line 33587. LaTeX Warning: Hyper reference `onlinehelp/gmx-densorder::doc' on page 293 unde fined on input line 33591. LaTeX Warning: Reference `onlinehelp/gmx-densorder::doc' on page 293 undefined on input line 33591. LaTeX Warning: Hyper reference `onlinehelp/gmx-h2order::doc' on page 293 undefi ned on input line 33595. LaTeX Warning: Reference `onlinehelp/gmx-h2order::doc' on page 293 undefined on input line 33595. LaTeX Warning: Hyper reference `onlinehelp/gmx-hydorder::doc' on page 293 undef ined on input line 33599. LaTeX Warning: Reference `onlinehelp/gmx-hydorder::doc' on page 293 undefined o n input line 33599. LaTeX Warning: Hyper reference `onlinehelp/gmx-order::doc' on page 293 undefine d on input line 33603. LaTeX Warning: Reference `onlinehelp/gmx-order::doc' on page 293 undefined on i nput line 33603. LaTeX Warning: Hyper reference `onlinehelp/gmx-potential::doc' on page 293 unde fined on input line 33607. LaTeX Warning: Reference `onlinehelp/gmx-potential::doc' on page 293 undefined on input line 33607. [293] LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig::doc' on page 294 undefin ed on input line 33616. LaTeX Warning: Reference `onlinehelp/gmx-anaeig::doc' on page 294 undefined on input line 33616. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar::doc' on page 294 undefine d on input line 33620. LaTeX Warning: Reference `onlinehelp/gmx-covar::doc' on page 294 undefined on i nput line 33620. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_edi::doc' on page 294 undef ined on input line 33624. LaTeX Warning: Reference `onlinehelp/gmx-make_edi::doc' on page 294 undefined o n input line 33624. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig::doc' on page 294 undefin ed on input line 33633. LaTeX Warning: Reference `onlinehelp/gmx-anaeig::doc' on page 294 undefined on input line 33633. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig::doc' on page 294 undefine d on input line 33637. LaTeX Warning: Reference `onlinehelp/gmx-nmeig::doc' on page 294 undefined on i nput line 33637. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmtraj::doc' on page 294 undefin ed on input line 33641. LaTeX Warning: Reference `onlinehelp/gmx-nmtraj::doc' on page 294 undefined on input line 33641. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmens::doc' on page 294 undefine d on input line 33645. LaTeX Warning: Reference `onlinehelp/gmx-nmens::doc' on page 294 undefined on i nput line 33645. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp::doc' on page 294 undefin ed on input line 33649. LaTeX Warning: Reference `onlinehelp/gmx-grompp::doc' on page 294 undefined on input line 33649. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 294 undefine d on input line 33653. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 294 undefined on i nput line 33653. [294] [295] [296] [297] [298] [299] [300] LaTeX Warning: Hyper reference `onlinehelp/selections::doc' on page 301 undefin ed on input line 34464. LaTeX Warning: Reference `onlinehelp/selections::doc' on page 301 undefined on input line 34464. [301] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 302 undefined on input line 34481. LaTeX Warning: Reference `release-notes/index:release-notes' on page 302 undefi ned on input line 34481. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-trj:gmx-convert-trj' on page 302 undefined on input line 34493. LaTeX Warning: Reference `onlinehelp/gmx-convert-trj:gmx-convert-trj' on page 3 02 undefined on input line 34493. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 302 undefined on input line 34494. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 302 undef ined on input line 34494. LaTeX Warning: Hyper reference `onlinehelp/gmx-extract-cluster:gmx-extract-clus ter' on page 302 undefined on input line 34503. LaTeX Warning: Reference `onlinehelp/gmx-extract-cluster:gmx-extract-cluster' o n page 302 undefined on input line 34503. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 302 undefined on input line 34505. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 302 undef ined on input line 34505. LaTeX Warning: Hyper reference `onlinehelp/gmx-trajectory:gmx-trajectory' on pa ge 302 undefined on input line 34517. LaTeX Warning: Reference `onlinehelp/gmx-trajectory:gmx-trajectory' on page 302 undefined on input line 34517. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 302 undef ined on input line 34518. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 302 undefined o n input line 34518. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 302 undefined on input line 34538. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 302 undefined on input line 34538. [302] LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 3 03 undefined on input line 34580. LaTeX Warning: Reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 303 und efined on input line 34580. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist:gmx-mindist' on page 303 undefined on input line 34581. LaTeX Warning: Reference `onlinehelp/gmx-mindist:gmx-mindist' on page 303 undef ined on input line 34581. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 303 undefin ed on input line 34593. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 303 undefined on input line 34593. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 03 undefined on input line 34649. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 303 und efined on input line 34649. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 03 undefined on input line 34652. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 303 und efined on input line 34652. [303] LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 04 undefined on input line 34684. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 304 und efined on input line 34684. LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 304 u ndefined on input line 34685. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 304 undefin ed on input line 34685. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 04 undefined on input line 34716. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 304 und efined on input line 34716. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 304 u ndefined on input line 34730. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 304 undefin ed on input line 34730. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 304 und efined on input line 34735. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 304 undefined on input line 34735. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 304 undefined on input line 34747. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 304 undef ined on input line 34747. [304] LaTeX Warning: Hyper reference `onlinehelp/gmx-sasa:gmx-sasa' on page 305 undef ined on input line 34769. LaTeX Warning: Reference `onlinehelp/gmx-sasa:gmx-sasa' on page 305 undefined o n input line 34769. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 305 u ndefined on input line 34806. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 305 undefin ed on input line 34806. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 05 undefined on input line 34807. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 305 und efined on input line 34807. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 3 05 undefined on input line 34830. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 305 und efined on input line 34830. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 305 undefined on input line 34838. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 305 undef ined on input line 34838. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 305 undefined on input line 34838. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 305 undefined on input line 34838. [305] LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 306 undefined on input line 34844. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 3 06 undefined on input line 34844. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undefined on input line 34934. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undef ined on input line 34934. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undefined on input line 34937. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undef ined on input line 34937. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undefined on input line 34939. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 306 undef ined on input line 34939. LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:pbc' on page 306 undefined on input line 34942. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:pbc' on page 306 undefined on input line 34942. [306] LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 307 undefined on input line 34948. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 307 undef ined on input line 34948. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 307 undefined on input line 34989. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 307 undef ined on input line 34989. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: temp-coupling' on page 307 undefined on input line 35038. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:temp-c oupling' on page 307 undefined on input line 35038. LaTeX Warning: Hyper reference `user-guide/terminology:what-not-to-do' on page 307 undefined on input line 35058. LaTeX Warning: Reference `user-guide/terminology:what-not-to-do' on page 307 un defined on input line 35058. LaTeX Warning: Hyper reference `user-guide/terminology:further-reading' on page 307 undefined on input line 35060. LaTeX Warning: Reference `user-guide/terminology:further-reading' on page 307 u ndefined on input line 35060. [307] LaTeX Warning: Hyper reference `user-guide/terminology:gmx-thermostats' on page 308 undefined on input line 35147. LaTeX Warning: Reference `user-guide/terminology:gmx-thermostats' on page 308 u ndefined on input line 35147. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-pressure' on page 30 8 undefined on input line 35147. LaTeX Warning: Reference `user-guide/terminology:gmx-pressure' on page 308 unde fined on input line 35147. [308] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 309 und efined on input line 35267. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 309 undefined on input line 35267. [309] LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 310 u ndefined on input line 35331. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 310 undefin ed on input line 35331. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undefined on input line 35338. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undef ined on input line 35338. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 310 u ndefined on input line 35338. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 310 undefin ed on input line 35338. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 310 undefined on input line 35345. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 310 undefi ned on input line 35345. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undefined on input line 35369. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undef ined on input line 35369. LaTeX Warning: Hyper reference `onlinehelp/gmx-genion:gmx-genion' on page 310 u ndefined on input line 35370. LaTeX Warning: Reference `onlinehelp/gmx-genion:gmx-genion' on page 310 undefin ed on input line 35370. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undefined on input line 35392. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 310 undef ined on input line 35392. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: md' on page 310 undefined on input line 35408. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:md' on page 310 undefined on input line 35408. [310] LaTeX Warning: Hyper reference `user-guide/terminology:gmx-thermostats' on page 311 undefined on input line 35474. LaTeX Warning: Reference `user-guide/terminology:gmx-thermostats' on page 311 u ndefined on input line 35474. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-pressure' on page 31 1 undefined on input line 35479. LaTeX Warning: Reference `user-guide/terminology:gmx-pressure' on page 311 unde fined on input line 35479. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 311 undefined on input line 35518. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 311 undefi ned on input line 35518. [311] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 312 undefined on input line 35566. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 312 undefi ned on input line 35566. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 312 undefined on input line 35578. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 312 undefi ned on input line 35578. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 312 undefined on input line 35578. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 312 undefi ned on input line 35578. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 312 undefined on input line 35579. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 312 undefi ned on input line 35579. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 312 undefined on input line 35608. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 312 undef ined on input line 35608. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 312 undefined on input line 35615. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 312 undef ined on input line 35615. [312] LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 313 undefined on input line 35690. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 313 undefi ned on input line 35690. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 313 undefined on input line 35691. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 313 undefi ned on input line 35691. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 313 und efined on input line 35699. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 313 undefined on input line 35699. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 313 und efined on input line 35705. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 313 undefined on input line 35705. [313] LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 314 undefined on input line 35769. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 314 undefi ned on input line 35769. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 314 un defined on input line 35812. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 314 undefine d on input line 35812. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 31 4 undefined on input line 35813. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 314 unde fined on input line 35813. [314] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 315 und efined on input line 35872. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 315 undefined on input line 35872. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 315 und efined on input line 35882. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 315 undefined on input line 35882. [315] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 316 undefined on input line 35966. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 316 undef ined on input line 35966. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 316 und efined on input line 35971. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 316 undefined on input line 35971. [316] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 317 und efined on input line 36023. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 317 undefined on input line 36023. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 3 17 undefined on input line 36023. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 317 und efined on input line 36023. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 3 17 undefined on input line 36027. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 317 und efined on input line 36027. [317] LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 318 undefined on input line 36140. LaTeX Warning: Reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 318 undef ined on input line 36140. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 318 u ndefined on input line 36144. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 318 undefin ed on input line 36144. LaTeX Warning: Hyper reference `onlinehelp/gmx-eneconv:gmx-eneconv' on page 318 undefined on input line 36144. LaTeX Warning: Reference `onlinehelp/gmx-eneconv:gmx-eneconv' on page 318 undef ined on input line 36144. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 318 u ndefined on input line 36150. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 318 undefin ed on input line 36150. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 318 undefined on input line 36155. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 318 undefi ned on input line 36155. [318] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 319 undefined on input line 36262. LaTeX Warning: Reference `release-notes/index:release-notes' on page 319 undefi ned on input line 36262. [319] Chapter 4. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-md' on page 320 unde fined on input line 36289. LaTeX Warning: Reference `user-guide/terminology:gmx-md' on page 320 undefined on input line 36289. LaTeX Warning: Hyper reference `reference-manual/index::doc' on page 320 undefi ned on input line 36298. LaTeX Warning: Reference `reference-manual/index::doc' on page 320 undefined on input line 36298. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-md' on page 320 unde fined on input line 36298. LaTeX Warning: Reference `user-guide/terminology:gmx-md' on page 320 undefined on input line 36298. LaTeX Warning: Hyper reference `user-guide/flow::doc' on page 320 undefined on input line 36302. LaTeX Warning: Reference `user-guide/flow::doc' on page 320 undefined on input line 36302. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 320 undefined on input line 36323. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 320 undef ined on input line 36323. LaTeX Warning: Hyper reference `reference-manual/index::doc' on page 320 undefi ned on input line 36324. LaTeX Warning: Reference `reference-manual/index::doc' on page 320 undefined on input line 36324. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 320 undefined on input line 36329. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 320 undefi ned on input line 36329. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 320 undefined on input line 36331. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 320 undefi ned on input line 36331. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 320 undefined on input line 36335. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 320 undefi ned on input line 36335. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 320 undefined on input line 36357. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 320 undefi ned on input line 36357. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 320 undefined on input line 36358. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 320 undefi ned on input line 36358. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 320 undefined on input line 36359. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 320 undefi ned on input line 36359. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 320 undefined on input line 36359. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 320 undefi ned on input line 36359. [320] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undefined on input line 36374. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undef ined on input line 36374. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undefined on input line 36376. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undef ined on input line 36376. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undefined on input line 36382. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undef ined on input line 36382. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undefined on input line 36383. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undef ined on input line 36383. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 321 undefined on input line 36390. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 321 undefi ned on input line 36390. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undefined on input line 36390. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 321 undef ined on input line 36390. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 321 undefined on input line 36391. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 321 undefi ned on input line 36391. LaTeX Warning: Hyper reference `how-to/topology:gmx-solvate-other' on page 321 undefined on input line 36395. LaTeX Warning: Reference `how-to/topology:gmx-solvate-other' on page 321 undefi ned on input line 36395. LaTeX Warning: Hyper reference `how-to/topology:gmx-solvate-mix' on page 321 un defined on input line 36395. LaTeX Warning: Reference `how-to/topology:gmx-solvate-mix' on page 321 undefine d on input line 36395. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undefined on input line 36403. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undef ined on input line 36403. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 3 21 undefined on input line 36415. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 321 und efined on input line 36415. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 3 21 undefined on input line 36416. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 321 und efined on input line 36416. LaTeX Warning: Hyper reference `onlinehelp/gmx-genconf:gmx-genconf' on page 321 undefined on input line 36417. LaTeX Warning: Reference `onlinehelp/gmx-genconf:gmx-genconf' on page 321 undef ined on input line 36417. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undefined on input line 36420. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undef ined on input line 36420. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 321 undefined on input line 36440. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 321 undefined on input line 36440. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undefined on input line 36444. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 321 undef ined on input line 36444. LaTeX Warning: Hyper reference `onlinehelp/gmx-insert-molecules:gmx-insert-mole cules' on page 321 undefined on input line 36444. LaTeX Warning: Reference `onlinehelp/gmx-insert-molecules:gmx-insert-molecules' on page 321 undefined on input line 36444. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 321 undefined on input line 36448. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 321 undefi ned on input line 36448. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 321 undefined on input line 36448. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 321 undefi ned on input line 36448. [321] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36458. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36458. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36458. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36458. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36459. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36459. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36460. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36460. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36461. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36461. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undefined on input line 36475. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 322 undef ined on input line 36475. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 322 undefined on input line 36480. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 322 undefi ned on input line 36480. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undefined on input line 36534. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undef ined on input line 36534. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undefined on input line 36547. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undef ined on input line 36547. LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undefined on input line 36553. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 322 undef ined on input line 36553. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 322 undefined on input line 36557. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 322 undefi ned on input line 36557. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 322 undefined on input line 36558. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 322 undefi ned on input line 36558. [322] LaTeX Warning: Hyper reference `user-guide/terminology:gmx-force-field' on page 323 undefined on input line 36607. LaTeX Warning: Reference `user-guide/terminology:gmx-force-field' on page 323 u ndefined on input line 36607. LaTeX Warning: Hyper reference `user-guide/system-preparation::doc' on page 323 undefined on input line 36622. LaTeX Warning: Reference `user-guide/system-preparation::doc' on page 323 undef ined on input line 36622. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 323 undefined on input line 36631. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 323 undefined on input line 36631. [323] LaTeX Warning: Hyper reference `onlinehelp/gmx-wham:gmx-wham' on page 324 undef ined on input line 36705. LaTeX Warning: Reference `onlinehelp/gmx-wham:gmx-wham' on page 324 undefined o n input line 36705. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 324 und efined on input line 36718. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 324 undefined on input line 36718. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 324 undefined on input line 36719. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 324 undefi ned on input line 36719. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 324 undefined on input line 36726. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 324 undefi ned on input line 36726. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 u ndefined on input line 36727. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 undefin ed on input line 36727. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 u ndefined on input line 36727. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 undefin ed on input line 36727. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 324 und efined on input line 36730. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 324 undefined on input line 36730. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 324 undefined on input line 36753. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 324 undefi ned on input line 36753. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 u ndefined on input line 36753. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 324 undefin ed on input line 36753. [324] LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36770. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36770. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36776. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36776. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36777. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36777. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 325 u ndefined on input line 36778. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 325 undefin ed on input line 36778. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 325 undefined on input line 36808. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 325 undefi ned on input line 36808. LaTeX Warning: Hyper reference `reference-manual/file-formats:n2t' on page 325 undefined on input line 36812. LaTeX Warning: Reference `reference-manual/file-formats:n2t' on page 325 undefi ned on input line 36812. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 325 undefined on input line 36816. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 325 undefi ned on input line 36816. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36822. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36822. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36823. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36823. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 und efined on input line 36834. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 325 undefined on input line 36834. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 325 undefined on input line 36845. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 325 undefi ned on input line 36845. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 325 undefined on input line 36845. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 325 undefi ned on input line 36845. [325] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 326 undefined on input line 36897. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 326 undefi ned on input line 36897. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 326 undefined on input line 36897. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 326 undefi ned on input line 36897. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 326 undefined on input line 36926. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 326 undefi ned on input line 36926. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 326 undefined on input line 36927. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 326 undefi ned on input line 36927. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 326 undefined on input line 36935. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 326 undefi ned on input line 36935. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 326 undefined on input line 36935. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 326 undefi ned on input line 36935. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 326 undefined on input line 36935. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 326 undefi ned on input line 36935. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 326 undef ined on input line 36943. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 326 undefined o n input line 36943. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 326 undefined on input line 36943. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 326 undefi ned on input line 36943. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 326 undef ined on input line 36951. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 326 undefined o n input line 36951. [326] LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 327 undefined on input line 36986. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 327 undefi ned on input line 36986. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 327 undefined on input line 36998. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 327 undefi ned on input line 36998. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 327 undefined on input line 37016. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 327 undefi ned on input line 37016. [327] LaTeX Warning: Hyper reference `onlinehelp/gmx-spatial:gmx-spatial' on page 328 undefined on input line 37065. LaTeX Warning: Reference `onlinehelp/gmx-spatial:gmx-spatial' on page 328 undef ined on input line 37065. LaTeX Warning: Hyper reference `user-guide/terminology:gmx-pbc' on page 328 und efined on input line 37069. LaTeX Warning: Reference `user-guide/terminology:gmx-pbc' on page 328 undefined on input line 37069. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 328 undefined on input line 37079. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 328 undef ined on input line 37079. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 328 u ndefined on input line 37085. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 328 undefin ed on input line 37085. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 328 undefined on input line 37085. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 328 undefi ned on input line 37085. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 328 undefined on input line 37089. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 328 undef ined on input line 37089. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 328 undefined on input line 37089. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 328 undefi ned on input line 37089. [328] Chapter 5. LaTeX Warning: Hyper reference `user-guide/index:user-guide' on page 329 undefi ned on input line 37112. LaTeX Warning: Reference `user-guide/index:user-guide' on page 329 undefined on input line 37112. LaTeX Warning: Hyper reference `install-guide/index:install-guide' on page 329 undefined on input line 37116. LaTeX Warning: Reference `install-guide/index:install-guide' on page 329 undefi ned on input line 37116. LaTeX Warning: Hyper reference `dev-manual/index:dev-guide' on page 329 undefin ed on input line 37120. LaTeX Warning: Reference `dev-manual/index:dev-guide' on page 329 undefined on input line 37120. LaTeX Warning: Hyper reference `dev-manual/contribute:gmx-contribute' on page 3 29 undefined on input line 37171. LaTeX Warning: Reference `dev-manual/contribute:gmx-contribute' on page 329 und efined on input line 37171. [329] LaTeX Warning: Hyper reference `reference-manual/references:refbekker93a' on pa ge 330 undefined on input line 37193. LaTeX Warning: Reference `reference-manual/references:refbekker93a' on page 330 undefined on input line 37193. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen95a' on page 330 undefined on input line 37197. LaTeX Warning: Reference `reference-manual/references:refberendsen95a' on page 330 undefined on input line 37197. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2001a' on page 330 undefined on input line 37201. LaTeX Warning: Reference `reference-manual/references:reflindahl2001a' on page 330 undefined on input line 37201. LaTeX Warning: Hyper reference `reference-manual/references:refspoel2005a' on p age 330 undefined on input line 37205. LaTeX Warning: Reference `reference-manual/references:refspoel2005a' on page 33 0 undefined on input line 37205. LaTeX Warning: Hyper reference `reference-manual/references:refhess2008b' on pa ge 330 undefined on input line 37209. LaTeX Warning: Reference `reference-manual/references:refhess2008b' on page 330 undefined on input line 37209. LaTeX Warning: Hyper reference `reference-manual/references:refpronk2013' on pa ge 330 undefined on input line 37213. LaTeX Warning: Reference `reference-manual/references:refpronk2013' on page 330 undefined on input line 37213. LaTeX Warning: Hyper reference `reference-manual/references:refpall2015' on pag e 330 undefined on input line 37217. LaTeX Warning: Reference `reference-manual/references:refpall2015' on page 330 undefined on input line 37217. LaTeX Warning: Hyper reference `reference-manual/references:refabraham2015' on page 330 undefined on input line 37221. LaTeX Warning: Reference `reference-manual/references:refabraham2015' on page 3 30 undefined on input line 37221. [330] LaTeX Warning: Hyper reference `reference-manual/references:refgunsteren90' on page 331 undefined on input line 37337. LaTeX Warning: Reference `reference-manual/references:refgunsteren90' on page 3 31 undefined on input line 37337. LaTeX Warning: Hyper reference `reference-manual/references:reffraaije93' on pa ge 331 undefined on input line 37340. LaTeX Warning: Reference `reference-manual/references:reffraaije93' on page 331 undefined on input line 37340. [331] LaTeX Warning: Hyper reference `reference-manual/introduction:tab-vibrations' o n page 332 undefined on input line 37431. LaTeX Warning: Reference `reference-manual/introduction:tab-vibrations' on page 332 undefined on input line 37431. LaTeX Warning: Hyper reference `reference-manual/references:refmcquarrie76' on page 332 undefined on input line 37559. LaTeX Warning: Reference `reference-manual/references:refmcquarrie76' on page 3 32 undefined on input line 37559. [332] LaTeX Warning: Hyper reference `reference-manual/references:refgunsteren77' on page 333 undefined on input line 37581. LaTeX Warning: Reference `reference-manual/references:refgunsteren77' on page 3 33 undefined on input line 37581. LaTeX Warning: Hyper reference `reference-manual/references:refgunsteren82' on page 333 undefined on input line 37584. LaTeX Warning: Reference `reference-manual/references:refgunsteren82' on page 3 33 undefined on input line 37584. LaTeX Warning: Hyper reference `reference-manual/references:refdarden93' on pag e 333 undefined on input line 37651. LaTeX Warning: Reference `reference-manual/references:refdarden93' on page 333 undefined on input line 37651. LaTeX Warning: Hyper reference `reference-manual/references:refessmann95' on pa ge 333 undefined on input line 37652. LaTeX Warning: Reference `reference-manual/references:refessmann95' on page 333 undefined on input line 37652. [333] LaTeX Warning: Hyper reference `reference-manual/introduction:compchem' on page 334 undefined on input line 37676. LaTeX Warning: Reference `reference-manual/introduction:compchem' on page 334 u ndefined on input line 37676. LaTeX Warning: Hyper reference `reference-manual/algorithms/energy-minimization :em' on page 334 undefined on input line 37678. LaTeX Warning: Reference `reference-manual/algorithms/energy-minimization:em' o n page 334 undefined on input line 37678. LaTeX Warning: Hyper reference `reference-manual/references:refgeman84' on page 334 undefined on input line 37704. LaTeX Warning: Reference `reference-manual/references:refgeman84' on page 334 u ndefined on input line 37704. LaTeX Warning: Hyper reference `reference-manual/references:refnilges88' on pag e 334 undefined on input line 37726. LaTeX Warning: Reference `reference-manual/references:refnilges88' on page 334 undefined on input line 37726. LaTeX Warning: Hyper reference `reference-manual/references:refschaik93' on pag e 334 undefined on input line 37729. LaTeX Warning: Reference `reference-manual/references:refschaik93' on page 334 undefined on input line 37729. LaTeX Warning: Hyper reference `reference-manual/references:refzimmerman91' on page 334 undefined on input line 37774. LaTeX Warning: Reference `reference-manual/references:refzimmerman91' on page 3 34 undefined on input line 37774. [334] [335] LaTeX Warning: Hyper reference `reference-manual/definitions:table-basicunits' on page 336 undefined on input line 37859. LaTeX Warning: Reference `reference-manual/definitions:table-basicunits' on pag e 336 undefined on input line 37859. LaTeX Warning: Hyper reference `reference-manual/definitions:table-derivedunits ' on page 336 undefined on input line 37945. LaTeX Warning: Reference `reference-manual/definitions:table-derivedunits' on p age 336 undefined on input line 37945. [336] LaTeX Warning: Hyper reference `reference-manual/definitions:table-derivedunits ' on page 337 undefined on input line 38071. LaTeX Warning: Reference `reference-manual/definitions:table-derivedunits' on p age 337 undefined on input line 38071. LaTeX Warning: Hyper reference `reference-manual/definitions:table-consts' on p age 337 undefined on input line 38092. LaTeX Warning: Reference `reference-manual/definitions:table-consts' on page 33 7 undefined on input line 38092. LaTeX Warning: Hyper reference `reference-manual/definitions:table-reduced' on page 337 undefined on input line 38200. LaTeX Warning: Reference `reference-manual/definitions:table-reduced' on page 3 37 undefined on input line 38200. [337] LaTeX Warning: Hyper reference `reference-manual/functions/long-range-vdw:viria l' on page 338 undefined on input line 38349. LaTeX Warning: Reference `reference-manual/functions/long-range-vdw:virial' on page 338 undefined on input line 38349. [338] LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:pbc' on page 339 undefined on input line 38383. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:pbc' on page 339 undefined on input line 38383. LaTeX Warning: Hyper reference `reference-manual/algorithms/group-concept:group concept' on page 339 undefined on input line 38384. LaTeX Warning: Reference `reference-manual/algorithms/group-concept:groupconcep t' on page 339 undefined on input line 38384. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: md' on page 339 undefined on input line 38385. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:md' on page 339 undefined on input line 38385. LaTeX Warning: Hyper reference `reference-manual/algorithms/energy-minimization :em' on page 339 undefined on input line 38387. LaTeX Warning: Reference `reference-manual/algorithms/energy-minimization:em' o n page 339 undefined on input line 38387. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 339 undefined on input line 38395. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 339 undefined on input line 38395. LaTeX Warning: Hyper reference `reference-manual/analysis/analysis:analysis' on page 339 undefined on input line 38399. LaTeX Warning: Reference `reference-manual/analysis/analysis:analysis' on page 339 undefined on input line 38399. LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:fig-pbc' on page 339 undefined on input line 38417. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:fig-pbc' on page 339 undefined on input line 38417. LaTeX Warning: Hyper reference `reference-manual/references:refadams79' on page 339 undefined on input line 38430. LaTeX Warning: Reference `reference-manual/references:refadams79' on page 339 u ndefined on input line 38430. LaTeX Warning: Hyper reference `reference-manual/references:refbekker95' on pag e 339 undefined on input line 38436. LaTeX Warning: Reference `reference-manual/references:refbekker95' on page 339 undefined on input line 38436. [339 <./pbctric.pdf>] LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 340 undefined on input line 38462. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxshift' on page 340 undefined on input line 38463. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxshift2' on page 340 undefined on input line 38464. LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:fig-pbc' on page 340 undefined on input line 38470. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:fig-pbc' on page 340 undefined on input line 38470. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 340 undefined on input line 38472. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 340 undef ined on input line 38472. [340 <./rhododec.pdf> <./truncoct.pdf pdfTeX warning: /usr/bin/pdflatex (file ./truncoct.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:table-boxtypes' on page 341 undefined on input line 38890. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:table-boxtypes' on page 341 undefined on input line 38890. LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:fig-boxshapes' on page 341 undefined on input line 38891. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:fig-boxshapes' on page 341 undefined on input line 38891. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 341 undefined on input line 38897. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxshift' on page 341 undefined on input line 38897. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxshift2' on page 341 undefined on input line 38898. LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 3 41 undefined on input line 38898. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 341 und efined on input line 38898. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: forces' on page 341 undefined on input line 38943. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:forces ' on page 341 undefined on input line 38943. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqngridrc' on page 341 undefined on input line 38944. [341] LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: update' on page 342 undefined on input line 38961. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:update ' on page 342 undefined on input line 38961. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 342 undefined on input line 39027. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 342 undefi ned on input line 39027. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 342 undefined on input line 39027. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 342 undefi ned on input line 39027. LaTeX Warning: Hyper reference `reference-manual/analysis/using-groups:usinggro ups' on page 342 undefined on input line 39037. LaTeX Warning: Reference `reference-manual/analysis/using-groups:usinggroups' o n page 342 undefined on input line 39037. [342] LaTeX Warning: Hyper reference `user-guide/index:user-guide' on page 343 undefi ned on input line 39101. LaTeX Warning: Reference `user-guide/index:user-guide' on page 343 undefined on input line 39101. LaTeX Warning: Hyper reference `user-guide/system-preparation:gmx-sysprep' on p age 343 undefined on input line 39102. LaTeX Warning: Reference `user-guide/system-preparation:gmx-sysprep' on page 34 3 undefined on input line 39102. LaTeX Warning: Hyper reference `user-guide/getting-started:gmx-getting-started' on page 343 undefined on input line 39102. LaTeX Warning: Reference `user-guide/getting-started:gmx-getting-started' on pa ge 343 undefined on input line 39102. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 343 undefined on input line 39112. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 343 undefined on input line 39112. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 343 undefined on input line 39113. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 343 undefi ned on input line 39113. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: update' on page 343 undefined on input line 39137. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:update ' on page 343 undefined on input line 39137. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: fig-maxwell' on page 343 undefined on input line 39142. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:fig-ma xwell' on page 343 undefined on input line 39142. [343] LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 344 undefined on input line 39148. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 344 un defined on input line 39148. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnET' on page 344 undefined on input line 39157. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 344 undefined on input line 39180. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 344 undefined on input line 39180. LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:fig-pbc' on page 344 undefined on input line 39184. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:fig-pbc' on page 344 undefined on input line 39184. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 344 undefined on input line 39187. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxshift2' on page 344 undefined on input line 39190. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnphysicalrc' on page 344 undefined on input line 39191. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqngridrc' on page 344 undefined on input line 39191. [344 <./maxwell.pdf>] LaTeX Warning: Hyper reference `reference-manual/algorithms/periodic-boundary-c onditions:pbc' on page 345 undefined on input line 39220. LaTeX Warning: Reference `reference-manual/algorithms/periodic-boundary-conditi ons:pbc' on page 345 undefined on input line 39220. LaTeX Warning: Hyper reference `reference-manual/references:refpallpairinteract ions' on page 345 undefined on input line 39264. LaTeX Warning: Reference `reference-manual/references:refpallpairinteractions' on page 345 undefined on input line 39264. [345]<> [346 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39411 ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqn2Ddisp' on page 347 undefined on input line 39433. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: fig-verletdrift' on page 347 undefined on input line 39481. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:fig-ve rletdrift' on page 347 undefined on input line 39481. [347 <./verlet-drift.pdf>] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 348 und efined on input line 39496. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 348 undefined on input line 39496. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:modnbint' on page 348 undefined on input line 39511. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:mod nbint' on page 348 undefined on input line 39511. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 348 und efined on input line 39534. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 348 undefined on input line 39534. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnverletanalytical' on page 348 undefined on input line 39536. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 348 undefined on input line 39556. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnsimplerc' on page 348 undefined on input line 39557. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 348 undefined on input line 39570. [348] LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: fig-grid' on page 349 undefined on input line 39586. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:fig-gr id' on page 349 undefined on input line 39586. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: fig-grid' on page 349 undefined on input line 39594. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:fig-gr id' on page 349 undefined on input line 39594. LaTeX Warning: Hyper reference `reference-manual/algorithms/group-concept:group concept' on page 349 undefined on input line 39627. LaTeX Warning: Reference `reference-manual/algorithms/group-concept:groupconcep t' on page 349 undefined on input line 39627. [349 <./nstric.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/long-range-vdw:viria l' on page 350 undefined on input line 39692. LaTeX Warning: Reference `reference-manual/functions/long-range-vdw:virial' on page 350 undefined on input line 39692. LaTeX Warning: Hyper reference `reference-manual/references:refhockney74' on pa ge 350 undefined on input line 39709. LaTeX Warning: Reference `reference-manual/references:refhockney74' on page 350 undefined on input line 39709. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: vverlet' on page 350 undefined on input line 39713. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:vverle t' on page 350 undefined on input line 39713. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: fig-leapfrog' on page 350 undefined on input line 39725. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:fig-le apfrog' on page 350 undefined on input line 39725. LaTeX Warning: Hyper reference `reference-manual/references:refverlet67' on pag e 350 undefined on input line 39726. LaTeX Warning: Reference `reference-manual/references:refverlet67' on page 350 undefined on input line 39726. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen86b' on page 350 undefined on input line 39733. LaTeX Warning: Reference `reference-manual/references:refberendsen86b' on page 350 undefined on input line 39733. [350 <./leapfrog.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refswope82' on page 351 undefined on input line 39746. LaTeX Warning: Reference `reference-manual/references:refswope82' on page 351 u ndefined on input line 39746. [351 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.31 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39816 \end{equation} ] LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqNVETrotter' on page 352 undefined on input line 39841. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 352 undefined on input line 39892. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 352 undefi ned on input line 39892. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv-avek' on page 352 undefined on input line 39893. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv-ave k' on page 352 undefined on input line 39893. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md' on page 352 undefined on input line 39904. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md' on pa ge 352 undefined on input line 39904. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv-avek' on page 352 undefined on input line 39904. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv-ave k' on page 352 undefined on input line 39904. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-md- vv' on page 352 undefined on input line 39907. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-md-vv' on page 352 undefined on input line 39907. [352 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.33 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 ] LaTeX Warning: Hyper reference `reference-manual/references:reftuckerman92' on page 353 undefined on input line 39950. LaTeX Warning: Reference `reference-manual/references:reftuckerman92' on page 3 53 undefined on input line 39950. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:rmfast ' on page 353 undefined on input line 39979. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:rmfast' on p age 353 undefined on input line 39979. [353] LaTeX Warning: Hyper reference `reference-manual/references:refberendsen84' on page 354 undefined on input line 39991. LaTeX Warning: Reference `reference-manual/references:refberendsen84' on page 3 54 undefined on input line 39991. LaTeX Warning: Hyper reference `reference-manual/references:refandersen80' on p age 354 undefined on input line 39992. LaTeX Warning: Reference `reference-manual/references:refandersen80' on page 35 4 undefined on input line 39992. LaTeX Warning: Hyper reference `reference-manual/references:refnose84' on page 354 undefined on input line 39993. LaTeX Warning: Reference `reference-manual/references:refnose84' on page 354 un defined on input line 39993. LaTeX Warning: Hyper reference `reference-manual/references:refhoover85' on pag e 354 undefined on input line 39993. LaTeX Warning: Reference `reference-manual/references:refhoover85' on page 354 undefined on input line 39993. LaTeX Warning: Hyper reference `reference-manual/references:refbussi2007a' on p age 354 undefined on input line 39994. LaTeX Warning: Reference `reference-manual/references:refbussi2007a' on page 35 4 undefined on input line 39994. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen91' on page 354 undefined on input line 40033. LaTeX Warning: Reference `reference-manual/references:refberendsen91' on page 3 54 undefined on input line 40033. LaTeX Warning: Hyper reference `reference-manual/references:refbussi2007a' on p age 354 undefined on input line 40057. LaTeX Warning: Reference `reference-manual/references:refbussi2007a' on page 35 4 undefined on input line 40057. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnTcoupling' on page 354 undefined on input line 40073. [354] LaTeX Warning: Hyper reference `reference-manual/references:refbussi2007a' on p age 355 undefined on input line 40105. LaTeX Warning: Reference `reference-manual/references:refbussi2007a' on page 35 5 undefined on input line 40105. LaTeX Warning: Hyper reference `reference-manual/references:refandersen80' on p age 355 undefined on input line 40126. LaTeX Warning: Reference `reference-manual/references:refandersen80' on page 35 5 undefined on input line 40126. LaTeX Warning: Hyper reference `reference-manual/references:refbasconi2013' on page 355 undefined on input line 40150. LaTeX Warning: Reference `reference-manual/references:refbasconi2013' on page 3 55 undefined on input line 40150. LaTeX Warning: Hyper reference `reference-manual/references:refnose84' on page 355 undefined on input line 40164. LaTeX Warning: Reference `reference-manual/references:refnose84' on page 355 un defined on input line 40164. LaTeX Warning: Hyper reference `reference-manual/references:refhoover85' on pag e 355 undefined on input line 40165. LaTeX Warning: Reference `reference-manual/references:refhoover85' on page 355 undefined on input line 40165. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: gmx-md-scheme' on page 355 undefined on input line 40176. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:gmx-md -scheme' on page 355 undefined on input line 40176. LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 355 undefined on input line 40190. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 355 un defined on input line 40190. [355] LaTeX Warning: Hyper reference `reference-manual/references:refcooke2008' on pa ge 356 undefined on input line 40249. LaTeX Warning: Reference `reference-manual/references:refcooke2008' on page 356 undefined on input line 40249. LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1992' on page 356 undefined on input line 40252. LaTeX Warning: Reference `reference-manual/references:refmartyna1992' on page 3 56 undefined on input line 40252. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 356 undefined on input line 40271. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 356 undefi ned on input line 40271. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 356 undefined on input line 40272. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 356 undefi ned on input line 40272. [356 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40283 ] LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1996' on page 357 undefined on input line 40288. LaTeX Warning: Reference `reference-manual/references:refmartyna1996' on page 3 57 undefined on input line 40288. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqhalfstepNHCintegrator' on page 357 undefined on input line 40326. LaTeX Warning: Hyper reference `reference-manual/references:refholian95' on pag e 357 undefined on input line 40335. LaTeX Warning: Reference `reference-manual/references:refholian95' on page 357 undefined on input line 40335. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 357 undefined on input line 40350. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 357 undefi ned on input line 40350. LaTeX Warning: Hyper reference `reference-manual/references:refeastwood2010' on page 357 undefined on input line 40355. LaTeX Warning: Reference `reference-manual/references:refeastwood2010' on page 357 undefined on input line 40355. LaTeX Warning: Hyper reference `reference-manual/references:refeastwood2010' on page 357 undefined on input line 40369. LaTeX Warning: Reference `reference-manual/references:refeastwood2010' on page 357 undefined on input line 40369. [357 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 ] LaTeX Warning: Hyper reference `reference-manual/references:refberendsen84' on page 358 undefined on input line 40377. LaTeX Warning: Reference `reference-manual/references:refberendsen84' on page 3 58 undefined on input line 40377. LaTeX Warning: Hyper reference `reference-manual/references:refparrinello81' on page 358 undefined on input line 40380. LaTeX Warning: Reference `reference-manual/references:refparrinello81' on page 358 undefined on input line 40380. LaTeX Warning: Hyper reference `reference-manual/references:refnose83' on page 358 undefined on input line 40380. LaTeX Warning: Reference `reference-manual/references:refnose83' on page 358 un defined on input line 40380. LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1996' on page 358 undefined on input line 40382. LaTeX Warning: Reference `reference-manual/references:refmartyna1996' on page 3 58 undefined on input line 40382. pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 358 undefined on input line 40414. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 358 un defined on input line 40414. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 358 undefined on input line 40417. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnXi' on page 358 undefined on input line 40442. [358] LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 359 undefined on input line 40502. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 359 un defined on input line 40502. LaTeX Warning: Hyper reference `reference-manual/references:refbernetti2020' on page 359 undefined on input line 40526. LaTeX Warning: Reference `reference-manual/references:refbernetti2020' on page 359 undefined on input line 40526. LaTeX Warning: Hyper reference `reference-manual/references:refparrinello81' on page 359 undefined on input line 40533. LaTeX Warning: Reference `reference-manual/references:refparrinello81' on page 359 undefined on input line 40533. LaTeX Warning: Hyper reference `reference-manual/references:refnose83' on page 359 undefined on input line 40534. LaTeX Warning: Reference `reference-manual/references:refnose83' on page 359 un defined on input line 40534. [359] LaTeX Warning: Hyper reference `reference-manual/references:refliu2015' on page 360 undefined on input line 40589. LaTeX Warning: Reference `reference-manual/references:refliu2015' on page 360 u ndefined on input line 40589. LaTeX Warning: Reference `equation:reference-manual/algorithms/periodic-boundar y-conditions:eqnboxrot' on page 360 undefined on input line 40595. [360] LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1996' on page 361 undefined on input line 40686. LaTeX Warning: Reference `reference-manual/references:refmartyna1996' on page 3 61 undefined on input line 40686. LaTeX Warning: Hyper reference `reference-manual/references:reftuckerman2006' o n page 361 undefined on input line 40687. LaTeX Warning: Reference `reference-manual/references:reftuckerman2006' on page 361 undefined on input line 40687. LaTeX Warning: Hyper reference `reference-manual/references:reftuckerman2006' o n page 361 undefined on input line 40693. LaTeX Warning: Reference `reference-manual/references:reftuckerman2006' on page 361 undefined on input line 40693. LaTeX Warning: Hyper reference `reference-manual/references:reftuckerman2006' o n page 361 undefined on input line 40713. LaTeX Warning: Reference `reference-manual/references:reftuckerman2006' on page 361 undefined on input line 40713. [361 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.63 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.65 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} ] LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1996' on page 362 undefined on input line 40772. LaTeX Warning: Reference `reference-manual/references:refmartyna1996' on page 3 62 undefined on input line 40772. [362 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} ] LaTeX Warning: Hyper reference `reference-manual/references:refyu2010' on page 363 undefined on input line 40838. LaTeX Warning: Reference `reference-manual/references:refyu2010' on page 363 un defined on input line 40838. LaTeX Warning: Hyper reference `reference-manual/references:refmartyna1996' on page 363 undefined on input line 40854. LaTeX Warning: Reference `reference-manual/references:refmartyna1996' on page 3 63 undefined on input line 40854. [363 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.69 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnlambda' on page 364 undefined on input line 40912. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnmu' on page 364 undefined on input line 40912. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: gmx-md-update' on page 364 undefined on input line 40947. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:gmx-md -update' on page 364 undefined on input line 40947. LaTeX Warning: Hyper reference `reference-manual/algorithms/group-concept:group concept' on page 364 undefined on input line 40955. LaTeX Warning: Reference `reference-manual/algorithms/group-concept:groupconcep t' on page 364 undefined on input line 40955. pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [364 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.41000 ] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 365 undefined on input line 41005. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 365 undefi ned on input line 41005. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 365 und efined on input line 41005. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 365 undefined on input line 41005. LaTeX Warning: Hyper reference `reference-manual/references:refdick58' on page 365 undefined on input line 41014. LaTeX Warning: Reference `reference-manual/references:refdick58' on page 365 un defined on input line 41014. LaTeX Warning: Hyper reference `reference-manual/references:refjordan95' on pag e 365 undefined on input line 41019. LaTeX Warning: Reference `reference-manual/references:refjordan95' on page 365 undefined on input line 41019. LaTeX Warning: Hyper reference `reference-manual/references:refmaaren2001a' on page 365 undefined on input line 41019. LaTeX Warning: Reference `reference-manual/references:refmaaren2001a' on page 3 65 undefined on input line 41019. LaTeX Warning: Hyper reference `reference-manual/references:refryckaert77' on p age 365 undefined on input line 41081. LaTeX Warning: Reference `reference-manual/references:refryckaert77' on page 36 5 undefined on input line 41081. [365] LaTeX Warning: Hyper reference `reference-manual/algorithms/constraint-algorith ms:settle' on page 366 undefined on input line 41122. LaTeX Warning: Reference `reference-manual/algorithms/constraint-algorithms:set tle' on page 366 undefined on input line 41122. LaTeX Warning: Hyper reference `reference-manual/references:refmiyamoto92' on p age 366 undefined on input line 41130. LaTeX Warning: Reference `reference-manual/references:refmiyamoto92' on page 36 6 undefined on input line 41130. LaTeX Warning: Hyper reference `reference-manual/topologies/constraint-algorith m-section:constraintalg' on page 366 undefined on input line 41131. LaTeX Warning: Reference `reference-manual/topologies/constraint-algorithm-sect ion:constraintalg' on page 366 undefined on input line 41131. LaTeX Warning: Hyper reference `reference-manual/references:refandersen1983a' o n page 366 undefined on input line 41148. LaTeX Warning: Reference `reference-manual/references:refandersen1983a' on page 366 undefined on input line 41148. LaTeX Warning: Hyper reference `reference-manual/references:refhess97' on page 366 undefined on input line 41158. LaTeX Warning: Reference `reference-manual/references:refhess97' on page 366 un defined on input line 41158. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:plincs' on page 366 undefined on input line 41166. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:plincs' on page 366 undefined on input line 41166. [366] Package amsmath Warning: Foreign command \over; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 41176. LaTeX Warning: Hyper reference `reference-manual/algorithms/constraint-algorith ms:fig-lincs' on page 367 undefined on input line 41189. LaTeX Warning: Reference `reference-manual/algorithms/constraint-algorithms:fig -lincs' on page 367 undefined on input line 41189. LaTeX Warning: Hyper reference `reference-manual/references:refhess97' on page 367 undefined on input line 41194. LaTeX Warning: Reference `reference-manual/references:refhess97' on page 367 un defined on input line 41194. LaTeX Warning: Reference `equation:reference-manual/algorithms/constraint-algor ithms:eqnc1' on page 367 undefined on input line 41232. LaTeX Warning: Reference `equation:reference-manual/algorithms/constraint-algor ithms:eqnc2' on page 367 undefined on input line 41233. LaTeX Warning: Hyper reference `reference-manual/references:refhess97' on page 367 undefined on input line 41233. LaTeX Warning: Reference `reference-manual/references:refhess97' on page 367 un defined on input line 41233. [367 <./lincs.pdf>] LaTeX Warning: Reference `equation:reference-manual/algorithms/constraint-algor ithms:eqnm3' on page 368 undefined on input line 41303. LaTeX Warning: Hyper reference `reference-manual/references:refhess2008a' on pa ge 368 undefined on input line 41324. LaTeX Warning: Reference `reference-manual/references:refhess2008a' on page 368 undefined on input line 41324. LaTeX Warning: Reference `equation:reference-manual/algorithms/constraint-algor ithms:eqnm3' on page 368 undefined on input line 41331. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 368 undefined on input line 41333. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 368 undefi ned on input line 41333. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 368 undefined on input line 41339. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 368 undefi ned on input line 41339. [368] LaTeX Warning: Hyper reference `reference-manual/references:refgoga2012' on pag e 369 undefined on input line 41404. LaTeX Warning: Reference `reference-manual/references:refgoga2012' on page 369 undefined on input line 41404. LaTeX Warning: Reference `equation:reference-manual/algorithms/stochastic-dynam ics:eqnsd1xupd' on page 369 undefined on input line 41427. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-sd' on page 369 undefined on input line 41432. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-sd' on pa ge 369 undefined on input line 41432. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 369 und efined on input line 41433. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 369 undefined on input line 41433. [369] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-bd' on page 370 undefined on input line 41473. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-bd' on pa ge 370 undefined on input line 41473. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 und efined on input line 41474. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 undefined on input line 41474. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 und efined on input line 41478. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 undefined on input line 41478. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-integrator' on page 370 undefined on input line 41496. LaTeX Warning: Reference `user-guide/mdp-options:mdp-integrator' on page 370 un defined on input line 41496. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 und efined on input line 41497. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 370 undefined on input line 41497. [370] LaTeX Warning: Hyper reference `reference-manual/references:refmiyamoto92' on p age 371 undefined on input line 41562. LaTeX Warning: Reference `reference-manual/references:refmiyamoto92' on page 37 1 undefined on input line 41562. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 371 undefined on input line 41564. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 371 undefi ned on input line 41564. LaTeX Warning: Hyper reference `reference-manual/references:refbyrd95a' on page 371 undefined on input line 41582. LaTeX Warning: Reference `reference-manual/references:refbyrd95a' on page 371 u ndefined on input line 41582. LaTeX Warning: Hyper reference `reference-manual/references:refzhu97a' on page 371 undefined on input line 41583. LaTeX Warning: Reference `reference-manual/references:refzhu97a' on page 371 un defined on input line 41583. LaTeX Warning: Hyper reference `reference-manual/references:reflevitt83' on pag e 371 undefined on input line 41600. LaTeX Warning: Reference `reference-manual/references:reflevitt83' on page 371 undefined on input line 41600. LaTeX Warning: Hyper reference `reference-manual/references:refbbrooks83b' on p age 371 undefined on input line 41600. LaTeX Warning: Reference `reference-manual/references:refbbrooks83b' on page 37 1 undefined on input line 41600. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 und efined on input line 41642. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 undefined on input line 41642. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 und efined on input line 41643. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 undefined on input line 41643. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 371 und efined on input line 41646. LaTeX Warning: Reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 371 undefined on input line 41646. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 und efined on input line 41648. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 371 undefined on input line 41648. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 371 und efined on input line 41648. LaTeX Warning: Reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 371 undefined on input line 41648. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 371 u ndefined on input line 41649. LaTeX Warning: Reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 371 undefin ed on input line 41649. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmens:gmx-nmens' on page 371 und efined on input line 41651. LaTeX Warning: Reference `onlinehelp/gmx-nmens:gmx-nmens' on page 371 undefined on input line 41651. LaTeX Warning: Hyper reference `reference-manual/analysis/covariance-analysis:c ovanal' on page 371 undefined on input line 41652. LaTeX Warning: Reference `reference-manual/analysis/covariance-analysis:covanal ' on page 371 undefined on input line 41652. LaTeX Warning: Hyper reference `reference-manual/references:refhayward95b' on p age 371 undefined on input line 41653. LaTeX Warning: Reference `reference-manual/references:refhayward95b' on page 37 1 undefined on input line 41653. [371] LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fig-free1' on page 372 undefined on input line 41672. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fig-free1' on page 372 undefined on input line 41672. LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fig-free2' on page 372 undefined on input line 41702. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fig-free2' on page 372 undefined on input line 41702. LaTeX Warning: Reference `equation:reference-manual/algorithms/free-energy-calc ulations:eqnddg' on page 372 undefined on input line 41703. [372 <./free1.pdf> <./free2.pdf pdfTeX warning: /usr/bin/pdflatex (file ./free2.pdf): PDF inclusion: multiple p dfs with page group included in a single page >] LaTeX Warning: Hyper reference `reference-manual/functions/free-energy-interact ions:feia' on page 373 undefined on input line 41731. LaTeX Warning: Reference `reference-manual/functions/free-energy-interactions:f eia' on page 373 undefined on input line 41731. [373] LaTeX Warning: Reference `equation:reference-manual/algorithms/free-energy-calc ulations:eqdelA' on page 374 undefined on input line 41810. LaTeX Warning: Reference `equation:reference-manual/algorithms/free-energy-calc ulations:eqdelG' on page 374 undefined on input line 41811. LaTeX Warning: Hyper reference `reference-manual/references:refbennett1976' on page 374 undefined on input line 41824. LaTeX Warning: Reference `reference-manual/references:refbennett1976' on page 3 74 undefined on input line 41824. LaTeX Warning: Hyper reference `onlinehelp/gmx-bar:gmx-bar' on page 374 undefin ed on input line 41825. LaTeX Warning: Reference `onlinehelp/gmx-bar:gmx-bar' on page 374 undefined on input line 41825. LaTeX Warning: Hyper reference `reference-manual/references:refshirts2008' on p age 374 undefined on input line 41826. LaTeX Warning: Reference `reference-manual/references:refshirts2008' on page 37 4 undefined on input line 41826. LaTeX Warning: Hyper reference `reference-manual/functions/free-energy-interact ions:feia' on page 374 undefined on input line 41832. LaTeX Warning: Reference `reference-manual/functions/free-energy-interactions:f eia' on page 374 undefined on input line 41832. LaTeX Warning: Hyper reference `reference-manual/references:refhukushima96a' on page 374 undefined on input line 41858. LaTeX Warning: Reference `reference-manual/references:refhukushima96a' on page 374 undefined on input line 41858. LaTeX Warning: Hyper reference `reference-manual/references:refsugita99' on pag e 374 undefined on input line 41859. LaTeX Warning: Reference `reference-manual/references:refsugita99' on page 374 undefined on input line 41859. LaTeX Warning: Hyper reference `reference-manual/references:refseibert2005a' on page 374 undefined on input line 41894. LaTeX Warning: Reference `reference-manual/references:refseibert2005a' on page 374 undefined on input line 41894. LaTeX Warning: Hyper reference `reference-manual/references:refokabe2001a' on p age 374 undefined on input line 41901. LaTeX Warning: Reference `reference-manual/references:refokabe2001a' on page 37 4 undefined on input line 41901. [374] LaTeX Warning: Hyper reference `reference-manual/references:refchodera2011' on page 375 undefined on input line 41934. LaTeX Warning: Reference `reference-manual/references:refchodera2011' on page 3 75 undefined on input line 41934. LaTeX Warning: Hyper reference `reference-manual/references:refchodera2011' on page 375 undefined on input line 41942. LaTeX Warning: Reference `reference-manual/references:refchodera2011' on page 3 75 undefined on input line 41942. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 375 undefined on input line 41954. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 375 undefi ned on input line 41954. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 und efined on input line 41955. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 undefined on input line 41955. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 und efined on input line 41958. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 undefined on input line 41958. LaTeX Warning: Hyper reference `reference-manual/analysis/covariance-analysis:c ovanal' on page 375 undefined on input line 41966. LaTeX Warning: Reference `reference-manual/analysis/covariance-analysis:covanal ' on page 375 undefined on input line 41966. LaTeX Warning: Hyper reference `reference-manual/references:refdegroot96a' on p age 375 undefined on input line 41975. LaTeX Warning: Reference `reference-manual/references:refdegroot96a' on page 37 5 undefined on input line 41975. LaTeX Warning: Hyper reference `reference-manual/references:refdegroot96b' on p age 375 undefined on input line 41975. LaTeX Warning: Reference `reference-manual/references:refdegroot96b' on page 37 5 undefined on input line 41975. LaTeX Warning: Hyper reference `reference-manual/references:reflange2006a' on p age 375 undefined on input line 41983. LaTeX Warning: Reference `reference-manual/references:reflange2006a' on page 37 5 undefined on input line 41983. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar:gmx-covar' on page 375 und efined on input line 41988. LaTeX Warning: Reference `onlinehelp/gmx-covar:gmx-covar' on page 375 undefined on input line 41988. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 375 und efined on input line 41988. LaTeX Warning: Reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 375 undefined on input line 41988. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_edi:gmx-make-edi' on page 3 75 undefined on input line 41989. LaTeX Warning: Reference `onlinehelp/gmx-make_edi:gmx-make-edi' on page 375 und efined on input line 41989. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 375 undefined on input line 41991. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 375 undefi ned on input line 41991. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 und efined on input line 41991. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 375 undefined on input line 41991. LaTeX Warning: Hyper reference `reference-manual/references:reflyubartsev1992' on page 375 undefined on input line 41999. LaTeX Warning: Reference `reference-manual/references:reflyubartsev1992' on pag e 375 undefined on input line 41999. [375] LaTeX Warning: Hyper reference `reference-manual/references:refliem1991' on pag e 376 undefined on input line 42060. LaTeX Warning: Reference `reference-manual/references:refliem1991' on page 376 undefined on input line 42060. LaTeX Warning: Hyper reference `reference-manual/references:refshaw2006' on pag e 376 undefined on input line 42060. LaTeX Warning: Reference `reference-manual/references:refshaw2006' on page 376 undefined on input line 42060. LaTeX Warning: Hyper reference `reference-manual/references:refhess2008b' on pa ge 376 undefined on input line 42065. LaTeX Warning: Reference `reference-manual/references:refhess2008b' on page 376 undefined on input line 42065. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:fig-ddcells' on page 376 undefined on input line 42090. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:fig-ddcells' on page 376 undefined on input line 42090. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:fig-ddcells' on page 376 undefined on input line 42105. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:fig-ddcells' on page 376 undefined on input line 42105. LaTeX Warning: Hyper reference `reference-manual/references:refhess2008b' on pa ge 376 undefined on input line 42108. LaTeX Warning: Reference `reference-manual/references:refhess2008b' on page 376 undefined on input line 42108. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:fig-ddtric' on page 376 undefined on input line 42144. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:fig-ddtric' on page 376 undefined on input line 42144. [376] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 und efined on input line 42160. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 undefined on input line 42160. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 und efined on input line 42177. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 undefined on input line 42177. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 und efined on input line 42204. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 377 undefined on input line 42204. [377 <./dd-cells.pdf> <./dd-tric.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dd-tric.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `reference-manual/references:refhess2008a' on pa ge 378 undefined on input line 42220. LaTeX Warning: Reference `reference-manual/references:refhess2008a' on page 378 undefined on input line 42220. LaTeX Warning: Hyper reference `reference-manual/references:refhess97' on page 378 undefined on input line 42221. LaTeX Warning: Reference `reference-manual/references:refhess97' on page 378 un defined on input line 42221. LaTeX Warning: Hyper reference `reference-manual/algorithms/constraint-algorith ms:id3' on page 378 undefined on input line 42221. LaTeX Warning: Reference `reference-manual/algorithms/constraint-algorithms:id3 ' on page 378 undefined on input line 42221. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:fig-plincs' on page 378 undefined on input line 42222. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:fig-plincs' on page 378 undefined on input line 42222. [378 <./par-lincs2.pdf>] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42249. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42249. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:table-ddranges' on page 379 undefined on input line 42253. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:table-ddranges' on page 379 undefined on input line 42253. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 379 undefined on input line 42342. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 379 undefi ned on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 379 undefined on input line 42342. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 379 undefi ned on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42342. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42342. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42347. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42347. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42370. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42370. LaTeX Warning: Hyper reference `reference-manual/functions/long-range-electrost atics:pme' on page 379 undefined on input line 42386. LaTeX Warning: Reference `reference-manual/functions/long-range-electrostatics: pme' on page 379 undefined on input line 42386. LaTeX Warning: Hyper reference `reference-manual/references:refhess2008b' on pa ge 379 undefined on input line 42390. LaTeX Warning: Reference `reference-manual/references:refhess2008b' on page 379 undefined on input line 42390. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42414. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42414. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42416. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42416. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42418. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42418. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 379 u ndefined on input line 42423. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 379 undefin ed on input line 42423. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42424. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42424. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 379 undefined on input line 42426. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 379 undefi ned on input line 42426. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 und efined on input line 42427. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 379 undefined on input line 42427. [379] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 380 und efined on input line 42442. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 380 undefined on input line 42442. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 380 und efined on input line 42449. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 380 undefined on input line 42449. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:fig-ddflow' on page 380 undefined on input line 42456. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:fig-ddflow' on page 380 undefined on input line 42456. [380 <./mpmd-pme.pdf>] [381 <./flowchart.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 382 undefined on input line 42479. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 382 undefined on input line 42479. LaTeX Warning: Hyper reference `reference-manual/special/special:special' on pa ge 382 undefined on input line 42509. LaTeX Warning: Reference `reference-manual/special/special:special' on page 382 undefined on input line 42509. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:fig-lj' on page 382 undefined on input line 42548. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:fig -lj' on page 382 undefined on input line 42548. [382] LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:fig-bham' on page 383 undefined on input line 42624. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:fig -bham' on page 383 undefined on input line 42624. [383 <./f-lj.pdf> <./f-bham.pdf pdfTeX warning: /usr/bin/pdflatex (file ./f-bham.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:fig-coul' on page 384 undefined on input line 42638. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:fig -coul' on page 384 undefined on input line 42638. LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 384 undefined on input line 42639. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 384 un defined on input line 42639. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 384 u ndefined on input line 42670. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 384 undefin ed on input line 42670. LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnvcrf' on page 384 undefined on input line 42690. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:fig-coul' on page 384 undefined on input line 42708. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:fig -coul' on page 384 undefined on input line 42708. [384 <./vcrf.pdf>] LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnvcrf' on page 385 undefined on input line 42718. LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnfcrf' on page 385 undefined on input line 42718. LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnvcrf' on page 385 undefined on input line 42758. [385] LaTeX Warning: Hyper reference `reference-manual/references:refohmine1988' on p age 386 undefined on input line 42880. LaTeX Warning: Reference `reference-manual/references:refohmine1988' on page 38 6 undefined on input line 42880. LaTeX Warning: Hyper reference `reference-manual/references:refguenot1993' on p age 386 undefined on input line 42880. LaTeX Warning: Reference `reference-manual/references:refguenot1993' on page 38 6 undefined on input line 42880. LaTeX Warning: Hyper reference `reference-manual/references:refsteinbach1994' o n page 386 undefined on input line 42881. LaTeX Warning: Reference `reference-manual/references:refsteinbach1994' on page 386 undefined on input line 42881. LaTeX Warning: Hyper reference `reference-manual/references:refspoel2006a' on p age 386 undefined on input line 42884. LaTeX Warning: Reference `reference-manual/references:refspoel2006a' on page 38 6 undefined on input line 42884. [386] LaTeX Warning: Hyper reference `reference-manual/functions/long-range-electrost atics:lrelstat' on page 387 undefined on input line 42903. LaTeX Warning: Reference `reference-manual/functions/long-range-electrostatics: lrelstat' on page 387 undefined on input line 42903. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-bstretch1' on page 387 undefined on input line 42927. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-bs tretch1' on page 387 undefined on input line 42927. LaTeX Warning: Hyper reference `reference-manual/references:refgromos96' on pag e 387 undefined on input line 42947. LaTeX Warning: Reference `reference-manual/references:refgromos96' on page 387 undefined on input line 42947. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: bondpot' on page 387 undefined on input line 42960. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:bondpo t' on page 387 undefined on input line 42960. LaTeX Warning: Hyper reference `reference-manual/references:refbiomos' on page 387 undefined on input line 42966. LaTeX Warning: Reference `reference-manual/references:refbiomos' on page 387 un defined on input line 42966. [387 <./bstretch.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refmorse29' on page 388 undefined on input line 42978. LaTeX Warning: Reference `reference-manual/references:refmorse29' on page 388 u ndefined on input line 42978. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-morse' on page 388 undefined on input line 42986. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-mo rse' on page 388 undefined on input line 42986. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnbetaij' on page 388 undefined on input line 43018. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnexpminx' on page 388 undefined on input line 43018. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen81' on page 388 undefined on input line 43048. LaTeX Warning: Reference `reference-manual/references:refberendsen81' on page 3 88 undefined on input line 43048. LaTeX Warning: Hyper reference `reference-manual/references:refferguson95' on p age 388 undefined on input line 43050. LaTeX Warning: Reference `reference-manual/references:refferguson95' on page 38 8 undefined on input line 43050. [388 <./f-morse.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refwarner72' on pag e 389 undefined on input line 43066. LaTeX Warning: Reference `reference-manual/references:refwarner72' on page 389 undefined on input line 43066. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-bstretch1' on page 389 undefined on input line 43088. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-bs tretch1' on page 389 undefined on input line 43088. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-angle' on page 389 undefined on input line 43118. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-an gle' on page 389 undefined on input line 43118. [389 <./angle.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: harmonicangle' on page 390 undefined on input line 43140. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:harmon icangle' on page 390 undefined on input line 43140. LaTeX Warning: Hyper reference `reference-manual/references:refmonicagoga2013' on page 390 undefined on input line 43155. LaTeX Warning: Reference `reference-manual/references:refmonicagoga2013' on pag e 390 undefined on input line 43155. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnG96angle' on page 390 undefined on input line 43163. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-reb' on page 390 undefined on input line 43169. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-re b' on page 390 undefined on input line 43169. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnReB' on page 390 undefined on input line 43170. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnG96angle' on page 390 undefined on input line 43170. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-reb' on page 390 undefined on input line 43207. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-re b' on page 390 undefined on input line 43207. [390 <./fig-02.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refbbrooks83' on pa ge 391 undefined on input line 43220. LaTeX Warning: Reference `reference-manual/references:refbbrooks83' on page 391 undefined on input line 43220. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: harmonicbond' on page 391 undefined on input line 43225. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:harmon icbond' on page 391 undefined on input line 43225. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: harmonicangle' on page 391 undefined on input line 43226. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:harmon icangle' on page 391 undefined on input line 43226. LaTeX Warning: Hyper reference `reference-manual/references:refspoel2020' on pa ge 391 undefined on input line 43233. LaTeX Warning: Reference `reference-manual/references:refspoel2020' on page 391 undefined on input line 43233. LaTeX Warning: Hyper reference `reference-manual/references:refspoel2020' on pa ge 391 undefined on input line 43254. LaTeX Warning: Reference `reference-manual/references:refspoel2020' on page 391 undefined on input line 43254. LaTeX Warning: Hyper reference `reference-manual/references:reflawrence2003b' o n page 391 undefined on input line 43262. LaTeX Warning: Reference `reference-manual/references:reflawrence2003b' on page 391 undefined on input line 43262. LaTeX Warning: Hyper reference `reference-manual/references:reflawrence2003b' o n page 391 undefined on input line 43286. LaTeX Warning: Reference `reference-manual/references:reflawrence2003b' on page 391 undefined on input line 43286. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqncrossbb' on page 391 undefined on input line 43293. [391] LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-imp' on page 392 undefined on input line 43331. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-im p' on page 392 undefined on input line 43331. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-imps' on page 392 undefined on input line 43362. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-im ps' on page 392 undefined on input line 43362. [392 <./ring-imp.pdf> <./subst-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./subst-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page > <./tetra-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./tetra-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 393 undefined on input line 43403. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 393 undef ined on input line 43403. [393 <./f-imps.pdf> <./f-dih.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-rbdih' on page 394 undefined on input line 43436. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-rb dih' on page 394 undefined on input line 43436. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: tab-crb' on page 394 undefined on input line 43462. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:tab-cr b' on page 394 undefined on input line 43462. [394 <./f-rbs.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen1996' o n page 395 undefined on input line 43574. LaTeX Warning: Reference `reference-manual/references:refjorgensen1996' on page 395 undefined on input line 43574. LaTeX Warning: Hyper reference `reference-manual/references:refrobertson2015a' on page 395 undefined on input line 43574. LaTeX Warning: Reference `reference-manual/references:refrobertson2015a' on pag e 395 undefined on input line 43574. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: reb' on page 395 undefined on input line 43596. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:reb' o n page 395 undefined on input line 43596. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: reb' on page 395 undefined on input line 43611. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:reb' o n page 395 undefined on input line 43611. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: reb' on page 395 undefined on input line 43622. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:reb' o n page 395 undefined on input line 43622. [395] LaTeX Warning: Hyper reference `reference-manual/references:refbulacugiessen200 5' on page 396 undefined on input line 43636. LaTeX Warning: Reference `reference-manual/references:refbulacugiessen2005' on page 396 undefined on input line 43636. LaTeX Warning: Hyper reference `reference-manual/references:refmonicagoga2013' on page 396 undefined on input line 43637. LaTeX Warning: Reference `reference-manual/references:refmonicagoga2013' on pag e 396 undefined on input line 43637. LaTeX Warning: Hyper reference `reference-manual/references:refscottscheragator 1966' on page 396 undefined on input line 43650. LaTeX Warning: Reference `reference-manual/references:refscottscheragator1966' on page 396 undefined on input line 43650. LaTeX Warning: Hyper reference `reference-manual/references:refpaulingbond' on page 396 undefined on input line 43651. LaTeX Warning: Reference `reference-manual/references:refpaulingbond' on page 3 96 undefined on input line 43651. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: fig-cbt' on page 396 undefined on input line 43671. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:fig-cb t' on page 396 undefined on input line 43671. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnCBT' on page 396 undefined on input line 43686. LaTeX Warning: Reference `equation:reference-manual/functions/bonded-interactio ns:eqnCBT' on page 396 undefined on input line 43686. [396 <./fig-04.pdf>] LaTeX Warning: Hyper reference `reference-manual/special/tabulated-interaction- functions:cubicspline' on page 397 undefined on input line 43754. LaTeX Warning: Reference `reference-manual/special/tabulated-interaction-functi ons:cubicspline' on page 397 undefined on input line 43754. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 397 undefined on input line 43758. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 397 undefined on input line 43758. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 397 und efined on input line 43759. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 397 undefined on input line 43759. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 397 undefined on input line 43765. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 397 undefined on input line 43765. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 397 undefined on input line 43770. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 397 undefined on input line 43770. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 397 und efined on input line 43772. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 397 undefined on input line 43772. [397] LaTeX Warning: Hyper reference `reference-manual/functions/restraints:fig-posit ionrestraint' on page 398 undefined on input line 43820. LaTeX Warning: Reference `reference-manual/functions/restraints:fig-positionres traint' on page 398 undefined on input line 43820. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 398 undefined on input line 43848. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 398 undef ined on input line 43848. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-refcoord-scali ng-all' on page 398 undefined on input line 43857. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-refcoord-scaling-all ' on page 398 undefined on input line 43857. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:fig-fbpos res' on page 398 undefined on input line 43870. LaTeX Warning: Reference `reference-manual/functions/restraints:fig-fbposres' o n page 398 undefined on input line 43870. [398 <./f-pr.pdf>] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 399 undefined on input line 43911. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 399 undefi ned on input line 43911. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:fig-fbpos res' on page 399 undefined on input line 43948. LaTeX Warning: Reference `reference-manual/functions/restraints:fig-fbposres' o n page 399 undefined on input line 43948. [399 <./fbposres.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: imp' on page 400 undefined on input line 43989. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:imp' o n page 400 undefined on input line 43989. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :excl' on page 400 undefined on input line 44024. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:excl' on page 400 undefined on input line 44024. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:fig-dist' on page 400 undefined on input line 44044. LaTeX Warning: Reference `reference-manual/functions/restraints:fig-dist' on pa ge 400 undefined on input line 44044. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 400 undefined on input line 44081. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 400 undefined on input line 44081. [400] LaTeX Warning: Hyper reference `reference-manual/references:reftorda89' on page 401 undefined on input line 44093. LaTeX Warning: Reference `reference-manual/references:reftorda89' on page 401 u ndefined on input line 44093. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 401 und efined on input line 44132. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 401 undefined on input line 44132. [401 <./f-dr.pdf>] LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqnrav ' on page 402 undefined on input line 44178. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 402 u ndefined on input line 44210. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 402 undefin ed on input line 44210. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:distancer estraint' on page 402 undefined on input line 44246. LaTeX Warning: Reference `reference-manual/functions/restraints:distancerestrai nt' on page 402 undefined on input line 44246. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqndis re' on page 402 undefined on input line 44257. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmr:gmx-nmr' on page 402 undefin ed on input line 44263. LaTeX Warning: Reference `onlinehelp/gmx-nmr:gmx-nmr' on page 402 undefined on input line 44263. [402] LaTeX Warning: Hyper reference `reference-manual/references:refhess2003' on pag e 403 undefined on input line 44273. LaTeX Warning: Reference `reference-manual/references:refhess2003' on page 403 undefined on input line 44273. [403] LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqnDro t' on page 404 undefined on input line 44381. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqnSms d' on page 404 undefined on input line 44399. [404] LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqnori entdef' on page 405 undefined on input line 44512. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 405 u ndefined on input line 44521. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 405 undefin ed on input line 44521. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 405 undefined on input line 44521. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 405 undefi ned on input line 44521. LaTeX Warning: Hyper reference `reference-manual/references:refhess2003' on pag e 405 undefined on input line 44522. LaTeX Warning: Reference `reference-manual/references:refhess2003' on page 405 undefined on input line 44522. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmr:gmx-nmr' on page 405 undefin ed on input line 44524. LaTeX Warning: Reference `onlinehelp/gmx-nmr:gmx-nmr' on page 405 undefined on input line 44524. [405] LaTeX Warning: Hyper reference `reference-manual/references:refmaaren2001a' on page 406 undefined on input line 44557. LaTeX Warning: Reference `reference-manual/references:refmaaren2001a' on page 4 06 undefined on input line 44557. LaTeX Warning: Hyper reference `reference-manual/references:reflopes2013a' on p age 406 undefined on input line 44569. LaTeX Warning: Reference `reference-manual/references:reflopes2013a' on page 40 6 undefined on input line 44569. LaTeX Warning: Hyper reference `reference-manual/references:refhyu2010' on page 406 undefined on input line 44579. LaTeX Warning: Reference `reference-manual/references:refhyu2010' on page 406 u ndefined on input line 44579. LaTeX Warning: Hyper reference `reference-manual/references:reflopes2013a' on p age 406 undefined on input line 44581. LaTeX Warning: Reference `reference-manual/references:reflopes2013a' on page 40 6 undefined on input line 44581. LaTeX Warning: Hyper reference `reference-manual/references:refmaaren2001a' on page 406 undefined on input line 44599. LaTeX Warning: Reference `reference-manual/references:refmaaren2001a' on page 4 06 undefined on input line 44599. LaTeX Warning: Hyper reference `reference-manual/references:refthole81' on page 406 undefined on input line 44605. LaTeX Warning: Reference `reference-manual/references:refthole81' on page 406 u ndefined on input line 44605. LaTeX Warning: Hyper reference `reference-manual/references:reflamoureux2003a' on page 406 undefined on input line 44607. LaTeX Warning: Reference `reference-manual/references:reflamoureux2003a' on pag e 406 undefined on input line 44607. LaTeX Warning: Hyper reference `reference-manual/references:refnoskov2005a' on page 406 undefined on input line 44607. LaTeX Warning: Reference `reference-manual/references:refnoskov2005a' on page 4 06 undefined on input line 44607. LaTeX Warning: Hyper reference `reference-manual/references:refnoskov2005a' on page 406 undefined on input line 44617. LaTeX Warning: Reference `reference-manual/references:refnoskov2005a' on page 4 06 undefined on input line 44617. LaTeX Warning: Hyper reference `reference-manual/references:refnoskov2005a' on page 406 undefined on input line 44623. LaTeX Warning: Reference `reference-manual/references:refnoskov2005a' on page 4 06 undefined on input line 44623. [406] LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fecalc' on page 407 undefined on input line 44634. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fecalc' on page 407 undefined on input line 44634. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 407 undefined on input line 44646. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 407 undefi ned on input line 44646. LaTeX Warning: Hyper reference `reference-manual/definitions:defunits' on page 407 undefined on input line 44723. LaTeX Warning: Reference `reference-manual/definitions:defunits' on page 407 un defined on input line 44723. [407 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} ] LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:coulrf' on page 408 undefined on input line 44742. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:cou lrf' on page 408 undefined on input line 44742. LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnsigeps' on page 408 undefined on input line 44761. LaTeX Warning: Hyper reference `reference-manual/references:refgunsteren98a' on page 408 undefined on input line 44777. LaTeX Warning: Reference `reference-manual/references:refgunsteren98a' on page 408 undefined on input line 44777. [408] LaTeX Warning: Reference `equation:reference-manual/functions/free-energy-inter actions:eqdVljdlambda' on page 409 undefined on input line 44849. LaTeX Warning: Reference `equation:reference-manual/functions/free-energy-inter actions:eqdVcoulombdlambda' on page 409 undefined on input line 44849. LaTeX Warning: Hyper reference `reference-manual/references:refbeutler94' on pa ge 409 undefined on input line 44869. LaTeX Warning: Reference `reference-manual/references:refbeutler94' on page 409 undefined on input line 44869. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 409 undefined on input line 44883. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 409 undefi ned on input line 44883. LaTeX Warning: Hyper reference `reference-manual/references:refbeutler94' on pa ge 409 undefined on input line 44887. LaTeX Warning: Reference `reference-manual/references:refbeutler94' on page 409 undefined on input line 44887. [409 <./softcore.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/free-energy-interact ions:fig-softcore' on page 410 undefined on input line 44896. LaTeX Warning: Reference `reference-manual/functions/free-energy-interactions:f ig-softcore' on page 410 undefined on input line 44896. LaTeX Warning: Hyper reference `reference-manual/references:refbeutler94' on pa ge 410 undefined on input line 44923. LaTeX Warning: Reference `reference-manual/references:refbeutler94' on page 410 undefined on input line 44923. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-coul' on page 410 undefined on input line 44941. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-coul' on page 410 undef ined on input line 44941. LaTeX Warning: Hyper reference `reference-manual/references:refgapsys2012' on p age 410 undefined on input line 44957. LaTeX Warning: Reference `reference-manual/references:refgapsys2012' on page 41 0 undefined on input line 44957. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-gapsys-scale-linp oint-q' on page 410 undefined on input line 44963. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-gapsys-scale-linpoint-q ' on page 410 undefined on input line 44963. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-sc-gapsys-scale-linp oint-lj' on page 410 undefined on input line 44963. LaTeX Warning: Reference `user-guide/mdp-options:mdp-sc-gapsys-scale-linpoint-l j' on page 410 undefined on input line 44963. LaTeX Warning: Hyper reference `reference-manual/functions/free-energy-interact ions:fig-gapsyssc' on page 410 undefined on input line 44965. LaTeX Warning: Reference `reference-manual/functions/free-energy-interactions:f ig-gapsyssc' on page 410 undefined on input line 44965. LaTeX Warning: Hyper reference `reference-manual/references:refgapsys2012' on p age 410 undefined on input line 44966. LaTeX Warning: Reference `reference-manual/references:refgapsys2012' on page 41 0 undefined on input line 44966. [410] [411 <./gapsys-sc.pdf>] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45084. [412] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45108. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-chain' on page 413 undefined on input line 45141. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-ch ain' on page 413 undefined on input line 45141. LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen88' on page 413 undefined on input line 45166. LaTeX Warning: Reference `reference-manual/references:refjorgensen88' on page 4 13 undefined on input line 45166. [413] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: tab-funcparm' on page 414 undefined on input line 45188. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:tab-fu ncparm' on page 414 undefined on input line 45188. LaTeX Warning: Hyper reference `reference-manual/algorithms/molecular-dynamics: gmx-md-pair-lists-generation' on page 414 undefined on input line 45189. LaTeX Warning: Reference `reference-manual/algorithms/molecular-dynamics:gmx-md -pair-lists-generation' on page 414 undefined on input line 45189. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen84b' on page 414 undefined on input line 45296. LaTeX Warning: Reference `reference-manual/references:refberendsen84b' on page 414 undefined on input line 45296. [414 <./chain.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refberendsen84b' on page 415 undefined on input line 45324. LaTeX Warning: Reference `reference-manual/references:refberendsen84b' on page 415 undefined on input line 45324. LaTeX Warning: Reference `equation:reference-manual/algorithms/molecular-dynami cs:eqnXi' on page 415 undefined on input line 45327. LaTeX Warning: Reference `equation:reference-manual/functions/interaction-metho ds:eqnfvsite' on page 415 undefined on input line 45330. pdfTeX warning: /usr/bin/pdflatex (file ./dummies.pdf): PDF inclusion: found PD F version <1.7>, but at most version <1.5> allowed LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 415 undefined on input line 45353. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 415 undefined on input line 45353. [415 <./dummies.pdf>] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 416 undefined on input line 45402. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 416 undefined on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45402. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 416 undefined on input line 45423. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 416 undefined on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45423. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 416 undefined on input line 45462. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 416 undefined on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45462. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 416 undefined on input line 45478. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 416 undefined on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45478. [416] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 417 undefined on input line 45520. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 417 undefined on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45520. LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:vsite top' on page 417 undefined on input line 45542. LaTeX Warning: Reference `reference-manual/topologies/particle-type:vsitetop' o n page 417 undefined on input line 45542. LaTeX Warning: Reference `equation:reference-manual/functions/interaction-metho ds:eqnvsite2fadF' on page 417 undefined on input line 45546. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsites' on page 417 undefined on input line 45600. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ites' on page 417 undefined on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45600. [417] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: fig-vsite4fdn' on page 418 undefined on input line 45639. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:fig-vs ite4fdn' on page 418 undefined on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. [418 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.27 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45729 <./vsite-4fdn.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refewald21' on page 419 undefined on input line 45761. LaTeX Warning: Reference `reference-manual/references:refewald21' on page 419 u ndefined on input line 45761. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-electr ostatics:eqntotalcoulomb' on page 419 undefined on input line 45762. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 419 undefined on input line 45793. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 419 undefi ned on input line 45793. [419] LaTeX Warning: Hyper reference `reference-manual/references:refdarden93' on pag e 420 undefined on input line 45818. LaTeX Warning: Reference `reference-manual/references:refdarden93' on page 420 undefined on input line 45818. LaTeX Warning: Hyper reference `reference-manual/references:refessmann95' on pa ge 420 undefined on input line 45821. LaTeX Warning: Reference `reference-manual/references:refessmann95' on page 420 undefined on input line 45821. LaTeX Warning: Hyper reference `reference-manual/algorithms/parallelization-dom ain-decomp:mpmdpme' on page 420 undefined on input line 45836. LaTeX Warning: Reference `reference-manual/algorithms/parallelization-domain-de comp:mpmdpme' on page 420 undefined on input line 45836. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 420 undefined on input line 45851. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 420 undefi ned on input line 45851. LaTeX Warning: Hyper reference `reference-manual/references:refhockney81' on pa ge 420 undefined on input line 45884. LaTeX Warning: Reference `reference-manual/references:refhockney81' on page 420 undefined on input line 45884. LaTeX Warning: Hyper reference `reference-manual/references:refballenegger2012' on page 420 undefined on input line 45895. LaTeX Warning: Reference `reference-manual/references:refballenegger2012' on pa ge 420 undefined on input line 45895. [420] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 421 und efined on input line 45921. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 421 undefined on input line 45921. LaTeX Warning: Hyper reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 4 21 undefined on input line 45923. LaTeX Warning: Reference `onlinehelp/gmx-tune_pme:gmx-tune-pme' on page 421 und efined on input line 45923. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq nenercorr' on page 421 undefined on input line 45982. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 421 undefined on input line 46000. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 421 u ndefined on input line 46000. [421] LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 422 undefined on input line 46054. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 422 u ndefined on input line 46054. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq navcsix' on page 422 undefined on input line 46065. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq npcorr' on page 422 undefined on input line 46070. LaTeX Warning: Hyper reference `reference-manual/functions/long-range-vdw:ecorr ' on page 422 undefined on input line 46071. LaTeX Warning: Reference `reference-manual/functions/long-range-vdw:ecorr' on p age 422 undefined on input line 46071. LaTeX Warning: Hyper reference `reference-manual/references:refessmann95' on pa ge 422 undefined on input line 46102. LaTeX Warning: Reference `reference-manual/references:refessmann95' on page 422 undefined on input line 46102. [422 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46108 \end{equation} ] LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqncomb' on page 423 undefined on input line 46111. LaTeX Warning: Reference `equation:reference-manual/functions/nonbonded-interac tions:eqnlorentzberthelot' on page 423 undefined on input line 46117. LaTeX Warning: Hyper reference `reference-manual/references:refwennberg13' on p age 423 undefined on input line 46145. LaTeX Warning: Reference `reference-manual/references:refwennberg13' on page 42 3 undefined on input line 46145. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq nljpmerealspace' on page 423 undefined on input line 46156. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq nljpmecorr2' on page 423 undefined on input line 46179. LaTeX Warning: Reference `equation:reference-manual/functions/long-range-vdw:eq nljpmedirectspace' on page 423 undefined on input line 46181. [423 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} ] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 424 undefined on input line 46197. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 424 undefi ned on input line 46197. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 424 und efined on input line 46238. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 424 undefined on input line 46238. [424] LaTeX Warning: Hyper reference `reference-manual/references:refgromos96' on pag e 425 undefined on input line 46299. LaTeX Warning: Reference `reference-manual/references:refgromos96' on page 425 undefined on input line 46299. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 425 undefined on input line 46303. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 425 undef ined on input line 46303. LaTeX Warning: Hyper reference `reference-manual/references:refoostenbrink2004' on page 425 undefined on input line 46309. LaTeX Warning: Reference `reference-manual/references:refoostenbrink2004' on pa ge 425 undefined on input line 46309. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: g96bond' on page 425 undefined on input line 46327. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:g96bon d' on page 425 undefined on input line 46327. LaTeX Warning: Hyper reference `reference-manual/functions/bonded-interactions: g96angle' on page 425 undefined on input line 46332. LaTeX Warning: Reference `reference-manual/functions/bonded-interactions:g96ang le' on page 425 undefined on input line 46332. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 425 undefined on input line 46367. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 425 undefi ned on input line 46367. LaTeX Warning: Hyper reference `reference-manual/references:refgromos96' on pag e 425 undefined on input line 46395. LaTeX Warning: Reference `reference-manual/references:refgromos96' on page 425 undefined on input line 46395. [425] LaTeX Warning: Hyper reference `reference-manual/references:refcornell1995' on page 426 undefined on input line 46410. LaTeX Warning: Reference `reference-manual/references:refcornell1995' on page 4 26 undefined on input line 46410. LaTeX Warning: Hyper reference `reference-manual/references:refkollman1996' on page 426 undefined on input line 46414. LaTeX Warning: Reference `reference-manual/references:refkollman1996' on page 4 26 undefined on input line 46414. LaTeX Warning: Hyper reference `reference-manual/references:refwang2000' on pag e 426 undefined on input line 46418. LaTeX Warning: Reference `reference-manual/references:refwang2000' on page 426 undefined on input line 46418. LaTeX Warning: Hyper reference `reference-manual/references:refhornak2006' on p age 426 undefined on input line 46422. LaTeX Warning: Reference `reference-manual/references:refhornak2006' on page 42 6 undefined on input line 46422. LaTeX Warning: Hyper reference `reference-manual/references:reflindorff2010' on page 426 undefined on input line 46426. LaTeX Warning: Reference `reference-manual/references:reflindorff2010' on page 426 undefined on input line 46426. LaTeX Warning: Hyper reference `reference-manual/references:refduan2003' on pag e 426 undefined on input line 46430. LaTeX Warning: Reference `reference-manual/references:refduan2003' on page 426 undefined on input line 46430. LaTeX Warning: Hyper reference `reference-manual/references:refgarcia2002' on p age 426 undefined on input line 46434. LaTeX Warning: Reference `reference-manual/references:refgarcia2002' on page 42 6 undefined on input line 46434. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undefined on input line 46441. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undef ined on input line 46441. LaTeX Warning: Hyper reference `reference-manual/references:refmackerell04' on page 426 undefined on input line 46480. LaTeX Warning: Reference `reference-manual/references:refmackerell04' on page 4 26 undefined on input line 46480. LaTeX Warning: Hyper reference `reference-manual/references:refmackerell98' on page 426 undefined on input line 46480. LaTeX Warning: Reference `reference-manual/references:refmackerell98' on page 4 26 undefined on input line 46480. LaTeX Warning: Hyper reference `reference-manual/references:reffeller00' on pag e 426 undefined on input line 46481. LaTeX Warning: Reference `reference-manual/references:reffeller00' on page 426 undefined on input line 46481. LaTeX Warning: Hyper reference `reference-manual/references:reffoloppe00' on pa ge 426 undefined on input line 46482. LaTeX Warning: Reference `reference-manual/references:reffoloppe00' on page 426 undefined on input line 46482. LaTeX Warning: Hyper reference `reference-manual/references:refmac2000' on page 426 undefined on input line 46482. LaTeX Warning: Reference `reference-manual/references:refmac2000' on page 426 u ndefined on input line 46482. LaTeX Warning: Hyper reference `reference-manual/references:reflarsson10' on pa ge 426 undefined on input line 46489. LaTeX Warning: Reference `reference-manual/references:reflarsson10' on page 426 undefined on input line 46489. LaTeX Warning: Hyper reference `reference-manual/references:refbjelkmar10' on p age 426 undefined on input line 46490. LaTeX Warning: Reference `reference-manual/references:refbjelkmar10' on page 42 6 undefined on input line 46490. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undefined on input line 46496. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undef ined on input line 46496. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undefined on input line 46514. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 426 undef ined on input line 46514. LaTeX Warning: Hyper reference `reference-manual/references:refkohlmeyer2016' o n page 426 undefined on input line 46515. LaTeX Warning: Reference `reference-manual/references:refkohlmeyer2016' on page 426 undefined on input line 46515. [426] LaTeX Warning: Hyper reference `reference-manual/references:refbereau12' on pag e 427 undefined on input line 46600. LaTeX Warning: Reference `reference-manual/references:refbereau12' on page 427 undefined on input line 46600. LaTeX Warning: Hyper reference `reference-manual/references:refwang-jpcb10' on page 427 undefined on input line 46602. LaTeX Warning: Reference `reference-manual/references:refwang-jpcb10' on page 4 27 undefined on input line 46602. LaTeX Warning: Hyper reference `reference-manual/functions/functions:ff' on pag e 427 undefined on input line 46613. LaTeX Warning: Reference `reference-manual/functions/functions:ff' on page 427 undefined on input line 46613. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 427 undefined on input line 46615. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 427 undefi ned on input line 46615. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 427 undefined on input line 46625. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 427 undefi ned on input line 46625. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 427 undefined on input line 46626. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 427 undefi ned on input line 46626. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 427 undefined on input line 46629. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 427 undefi ned on input line 46629. LaTeX Warning: Hyper reference `reference-manual/topologies/force-field-organiz ation:fffiles' on page 427 undefined on input line 46632. LaTeX Warning: Reference `reference-manual/topologies/force-field-organization: fffiles' on page 427 undefined on input line 46632. [427] LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:tab-p type' on page 428 undefined on input line 46650. LaTeX Warning: Reference `reference-manual/topologies/particle-type:tab-ptype' on page 428 undefined on input line 46650. LaTeX Warning: Hyper reference `reference-manual/references:refmaaren2001a' on page 428 undefined on input line 46652. LaTeX Warning: Reference `reference-manual/references:refmaaren2001a' on page 4 28 undefined on input line 46652. LaTeX Warning: Hyper reference `reference-manual/file-formats:atp' on page 428 undefined on input line 46705. LaTeX Warning: Reference `reference-manual/file-formats:atp' on page 428 undefi ned on input line 46705. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 428 undefined on input line 46708. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 428 undef ined on input line 46708. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: virtualsites' on page 428 undefined on input line 46754. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:virtua lsites' on page 428 undefined on input line 46754. LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: virtualsites' on page 428 undefined on input line 46767. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:virtua lsites' on page 428 undefined on input line 46767. [428] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 429 u ndefined on input line 46856. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 429 undefin ed on input line 46856. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 429 undefined on input line 46864. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 429 undefined on input line 46864. [429] LaTeX Warning: Hyper reference `reference-manual/topologies/parameter-files:tab -statprop' on page 430 undefined on input line 46883. LaTeX Warning: Reference `reference-manual/topologies/parameter-files:tab-statp rop' on page 430 undefined on input line 46883. LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:atomt ype' on page 430 undefined on input line 46885. LaTeX Warning: Reference `reference-manual/topologies/particle-type:atomtype' o n page 430 undefined on input line 46885. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 430 undefined on input line 46886. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 430 undefi ned on input line 46886. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 430 undefined on input line 46886. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 430 undefi ned on input line 46886. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 430 undefined on input line 46887. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 430 undefi ned on input line 46887. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 430 undefined on input line 46889. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 430 undefi ned on input line 46889. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 430 undefined on input line 46889. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 430 undef ined on input line 46889. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:lj' on page 430 undefined on input line 46973. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:lj' on page 430 undefined on input line 46973. LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:tab-p type' on page 430 undefined on input line 46975. LaTeX Warning: Reference `reference-manual/topologies/particle-type:tab-ptype' on page 430 undefined on input line 46975. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :pairinteractions' on page 430 undefined on input line 46978. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:pairi nteractions' on page 430 undefined on input line 46978. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 430 undefined on input line 46999. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 430 undefined on input line 46999. [430] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 431 u ndefined on input line 47065. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 431 undefin ed on input line 47065. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 431 undefined on input line 47071. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 431 undefined on input line 47071. [431] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 432 undefined on input line 47158. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 432 undefi ned on input line 47158. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 432 undefined on input line 47171. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 432 undef ined on input line 47171. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile1' on page 432 undefined on input line 47177. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile1' on page 432 undefined on input line 47177. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :excl' on page 432 undefined on input line 47193. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:excl' on page 432 undefined on input line 47193. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 432 undefined on input line 47210. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 432 undefined on input line 47210. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 432 u ndefined on input line 47211. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 432 undefin ed on input line 47211. [432] LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fecalc' on page 433 undefined on input line 47219. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fecalc' on page 433 undefined on input line 47219. LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fecalc' on page 433 undefined on input line 47240. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fecalc' on page 433 undefined on input line 47240. LaTeX Warning: Hyper reference `reference-manual/special/free-energy-implementa tion:dgimplement' on page 433 undefined on input line 47240. LaTeX Warning: Reference `reference-manual/special/free-energy-implementation:d gimplement' on page 433 undefined on input line 47240. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 433 u ndefined on input line 47254. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 433 undefin ed on input line 47254. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 433 undefined on input line 47256. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 433 undefined on input line 47256. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 433 undefined on input line 47263. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 433 undefined on input line 47263. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :excl' on page 433 undefined on input line 47281. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:excl' on page 433 undefined on input line 47281. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 433 undefined on input line 47283. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 433 undefi ned on input line 47283. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:constraintforce' on page 433 undefined on input line 47285. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:con straintforce' on page 433 undefined on input line 47285. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 433 undefined on input line 47286. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 433 undefined on input line 47286. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 433 u ndefined on input line 47287. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 433 undefin ed on input line 47287. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 433 undefined on input line 47287. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 433 undefi ned on input line 47287. LaTeX Warning: Hyper reference `reference-manual/references:refmiyamoto92' on p age 433 undefined on input line 47292. LaTeX Warning: Reference `reference-manual/references:refmiyamoto92' on page 43 3 undefined on input line 47292. [433] LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen83' on page 434 undefined on input line 47321. LaTeX Warning: Reference `reference-manual/references:refjorgensen83' on page 4 34 undefined on input line 47321. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47331. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47331. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 434 undefined on input line 47333. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 434 undefi ned on input line 47333. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47333. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47333. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47334. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47334. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47338. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47338. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47340. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47340. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47341. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47341. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47346. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47346. LaTeX Warning: Hyper reference `reference-manual/file-formats:atp' on page 434 undefined on input line 47347. LaTeX Warning: Reference `reference-manual/file-formats:atp' on page 434 undefi ned on input line 47347. LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:atomt ype' on page 434 undefined on input line 47347. LaTeX Warning: Reference `reference-manual/topologies/particle-type:atomtype' o n page 434 undefined on input line 47347. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47353. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47353. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 434 undefined on input line 47386. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 434 undefi ned on input line 47386. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 434 undefined on input line 47388. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 434 undefi ned on input line 47388. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undefined on input line 47391. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 434 undef ined on input line 47391. [434] LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 435 undefined on input line 47399. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 435 undefi ned on input line 47399. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 435 undefined on input line 47405. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 435 undef ined on input line 47405. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 435 undefined on input line 47406. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 435 undefi ned on input line 47406. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 435 undefined on input line 47406. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 435 undefined on input line 47406. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 435 undefined on input line 47406. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 435 undefi ned on input line 47406. LaTeX Warning: Hyper reference `reference-manual/topologies/pdb2gmx-input-files :pdb2gmxfiles' on page 435 undefined on input line 47407. LaTeX Warning: Reference `reference-manual/topologies/pdb2gmx-input-files:pdb2g mxfiles' on page 435 undefined on input line 47407. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 435 undefined on input line 47409. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 435 undefi ned on input line 47409. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:molitp' on page 435 undefined on input line 47409. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:mol itp' on page 435 undefined on input line 47409. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 435 u ndefined on input line 47411. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 435 undefin ed on input line 47411. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 4 35 undefined on input line 47411. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 435 und efined on input line 47411. LaTeX Warning: Hyper reference `reference-manual/analysis/using-groups:defaultg roups' on page 435 undefined on input line 47413. LaTeX Warning: Reference `reference-manual/analysis/using-groups:defaultgroups' on page 435 undefined on input line 47413. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 435 undefined on input line 47416. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 435 undefi ned on input line 47416. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 435 undefined on input line 47416. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 435 undef ined on input line 47416. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 435 undefined on input line 47417. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 435 undefi ned on input line 47417. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 435 undefined on input line 47422. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 435 undefi ned on input line 47422. Underfull \vbox (badness 2368) detected at line 47468 [435] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47478. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47478. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 436 undefined on input line 47479. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 436 undefi ned on input line 47479. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 436 undefined on input line 47479. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 436 undefi ned on input line 47479. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 436 undefined on input line 47485. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 436 undefi ned on input line 47485. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 436 undefined on input line 47487. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 436 undefi ned on input line 47487. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 436 u ndefined on input line 47489. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 436 undefin ed on input line 47489. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47492. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47492. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 436 undefined on input line 47494. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 436 undefi ned on input line 47494. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47498. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47498. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47502. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47502. LaTeX Warning: Hyper reference `reference-manual/functions/force-field:charmmff ' on page 436 undefined on input line 47504. LaTeX Warning: Reference `reference-manual/functions/force-field:charmmff' on p age 436 undefined on input line 47504. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47507. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47507. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 436 undefined on input line 47523. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 436 undefi ned on input line 47523. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 436 undefined on input line 47524. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 436 undefi ned on input line 47524. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 436 undefined on input line 47527. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 436 undefi ned on input line 47527. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undefined on input line 47538. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 436 undef ined on input line 47538. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 436 undefined on input line 47539. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 436 undefi ned on input line 47539. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 436 undefined on input line 47541. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 436 undefi ned on input line 47541. LaTeX Warning: Hyper reference `reference-manual/topologies/pdb2gmx-input-files :tab-r2b' on page 436 undefined on input line 47541. LaTeX Warning: Reference `reference-manual/topologies/pdb2gmx-input-files:tab-r 2b' on page 436 undefined on input line 47541. LaTeX Warning: Hyper reference `reference-manual/topologies/pdb2gmx-input-files :specbond' on page 436 undefined on input line 47544. LaTeX Warning: Reference `reference-manual/topologies/pdb2gmx-input-files:specb ond' on page 436 undefined on input line 47544. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 436 undefined on input line 47545. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 436 undefi ned on input line 47545. [436] LaTeX Warning: Hyper reference `reference-manual/file-formats:arn' on page 437 undefined on input line 47745. LaTeX Warning: Reference `reference-manual/file-formats:arn' on page 437 undefi ned on input line 47745. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 437 undefined on input line 47765. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 437 undefi ned on input line 47765. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 437 undefined on input line 47766. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 437 undef ined on input line 47766. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 437 undefined on input line 47776. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 437 undefi ned on input line 47776. [437] LaTeX Warning: Hyper reference `reference-manual/references:refiupac70' on page 438 undefined on input line 47830. LaTeX Warning: Reference `reference-manual/references:refiupac70' on page 438 u ndefined on input line 47830. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen81' on page 438 undefined on input line 47865. LaTeX Warning: Reference `reference-manual/references:refberendsen81' on page 4 38 undefined on input line 47865. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen81' on page 438 undefined on input line 47874. LaTeX Warning: Reference `reference-manual/references:refberendsen81' on page 4 38 undefined on input line 47874. LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen83' on page 438 undefined on input line 47879. LaTeX Warning: Reference `reference-manual/references:refjorgensen83' on page 4 38 undefined on input line 47879. LaTeX Warning: Hyper reference `reference-manual/references:refmahoney2000a' on page 438 undefined on input line 47888. LaTeX Warning: Reference `reference-manual/references:refmahoney2000a' on page 438 undefined on input line 47888. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 438 undefined on input line 47923. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 438 undef ined on input line 47923. [438] LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 439 undefined on input line 47975. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 439 undefi ned on input line 47975. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 439 undefined on input line 47982. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 439 undef ined on input line 47982. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 439 undefined on input line 48014. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 439 undefi ned on input line 48014. [439] LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 440 undefined on input line 48065. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 440 undefi ned on input line 48065. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 440 undefined on input line 48085. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 440 undefi ned on input line 48085. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 440 undefined on input line 48085. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 440 undefi ned on input line 48085. LaTeX Warning: Hyper reference `reference-manual/file-formats:vsd' on page 440 undefined on input line 48100. LaTeX Warning: Reference `reference-manual/file-formats:vsd' on page 440 undefi ned on input line 48100. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 440 undefined on input line 48102. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 440 undefi ned on input line 48102. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 440 undefined on input line 48143. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 440 undef ined on input line 48143. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 440 undefined on input line 48153. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 440 undef ined on input line 48153. Underfull \hbox (badness 10000) in paragraph at lines 48166--48169 []\T1/pcr/m/n/10 resA atomA nbondsA resB atomB nbondsB length newresA newresB [ atomI atomJ [440] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 441 undefined on input line 48209. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 441 undef ined on input line 48209. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 441 undefined on input line 48253. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 441 undefi ned on input line 48253. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 441 undefined on input line 48254. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 441 undef ined on input line 48254. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile1' on page 441 undefined on input line 48255. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile1' on page 441 undefined on input line 48255. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48256. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48256. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 441 u ndefined on input line 48259. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 441 undefin ed on input line 48259. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 441 u ndefined on input line 48260. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 441 undefin ed on input line 48260. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48340. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48340. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48353. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48353. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48366. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48366. Overfull \hbox (10.25368pt too wide) in paragraph at lines 48373--48375 []|\T1/pcr/m/n/10 dihedraltypes$[]$| LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48379. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48379. Overfull \hbox (11.40642pt too wide) in paragraph at lines 48386--48388 []|\T1/pcr/m/n/10 constrainttypes| LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 441 undefined on input line 48392. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 441 undefined on input line 48392. Underfull \hbox (badness 10000) in paragraph at lines 48402--48404 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48418--48420 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ [441] Underfull \hbox (badness 10000) in paragraph at lines 48468--48470 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 48481--48485 \T1/ptm/m/n/10 num-ber; residue LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 442 undefined on input line 48495. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 442 undefined on input line 48495. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 442 undefined on input line 48569. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 442 undefined on input line 48569. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 442 undefined on input line 48569. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 442 undefined on input line 48569. LaTeX Warning: Hyper reference `reference-manual/topologies/parameter-files:nbp ar' on page 442 undefined on input line 48587. LaTeX Warning: Reference `reference-manual/topologies/parameter-files:nbpar' on page 442 undefined on input line 48587. [442] Underfull \hbox (badness 10000) in paragraph at lines 48619--48621 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 48648--48650 []|\T1/phv/m/n/10 Topol-ogy file LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 443 u ndefined on input line 48696. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 443 undefin ed on input line 48696. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 443 u ndefined on input line 48700. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 443 undefin ed on input line 48700. Underfull \hbox (badness 10000) in paragraph at lines 48748--48750 []|$\OML/cmm/m/it/10 b[]$ \T1/ptm/m/n/10 (nm); $\OML/cmm/m/it/10 D$ Underfull \hbox (badness 10000) in paragraph at lines 48784--48786 []|\T1/ptm/m/n/10 har-monic Underfull \hbox (badness 10000) in paragraph at lines 48831--48833 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48854--48856 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48873--48875 []|\T1/ptm/m/n/10 low, up$[]$,$[]$ Underfull \hbox (badness 10000) in paragraph at lines 48880--48882 []|\T1/ptm/m/n/10 ex-tra LJ or LaTeX Warning: Hyper reference `reference-manual/topologies/parameter-files:nbp ar' on page 443 undefined on input line 48895. LaTeX Warning: Reference `reference-manual/topologies/parameter-files:nbpar' on page 443 undefined on input line 48895. Underfull \hbox (badness 10000) in paragraph at lines 48903--48905 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48919--48921 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48973--48975 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 10000) in paragraph at lines 48985--48987 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 48989--48991 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 6542) in paragraph at lines 49001--49003 []|$\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$ Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \T1/ptm/m/n/10 mol$[]$rad$[]$); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 r[]$ \T1/ptm/m/n/10 (nm); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 49036--49038 []|$\OML/cmm/m/it/10 ^^R[]$ \T1/ptm/m/n/10 (deg); Underfull \hbox (badness 10000) in paragraph at lines 49052--49054 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 5592) in paragraph at lines 49071--49073 []|$\OML/cmm/m/it/10 a[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 []|\T1/ptm/m/n/10 Ryckaert- Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 \T1/ptm/m/n/10 Bellemans Underfull \hbox (badness 7888) in paragraph at lines 49146--49148 []|$\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 49153--49155 []|\T1/ptm/m/n/10 pe-ri-odic im- Underfull \hbox (badness 10000) in paragraph at lines 49172--49174 []|\T1/ptm/m/n/10 Fourier di-he- Underfull \hbox (badness 10000) in paragraph at lines 49203--49205 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 []|\T1/ptm/m/n/10 com-bined Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 \T1/ptm/m/n/10 bending-torsion Underfull \hbox (badness 10000) in paragraph at lines 49270--49272 []|\T1/ptm/m/n/10 one or more Overfull \hbox (6.11331pt too wide) in paragraph at lines 49277--49279 []|\T1/pcr/m/n/10 constraints[][][]| Overfull \hbox (2.50536pt too wide) in paragraph at lines 49296--49298 []|\T1/pcr/m/n/10 constraints| Underfull \hbox (badness 10000) in paragraph at lines 49328--49330 []|\T1/ptm/m/n/10 1-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49331--49333 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49341--49343 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49344--49346 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49357--49359 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49360--49362 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49373--49375 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49376--49378 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49389--49391 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49392--49394 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49405--49407 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49408--49410 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49421--49423 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49424--49426 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49433--49435 []|$\OML/cmm/m/it/10 a$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 (); $\OML/cmm/m/it/10 c$ Underfull \hbox (badness 10000) in paragraph at lines 49437--49439 []|\T1/ptm/m/n/10 4-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49440--49442 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49456--49458 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49472--49474 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49488--49490 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49503--49505 []|\T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49506--49508 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 []|\T1/ptm/m/n/10 flat-bottomed Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 \T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49525--49527 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49538--49540 []|\T1/ptm/m/n/10 dis-tance re- Underfull \hbox (badness 10000) in paragraph at lines 49541--49543 []|\T1/pcr/m/n/10 distance_- Underfull \hbox (badness 10000) in paragraph at lines 49550--49552 \T1/ptm/m/n/10 up$[]$,$[]$ (nm); Underfull \hbox (badness 10000) in paragraph at lines 49554--49556 []|\T1/ptm/m/n/10 di-he-dral re- Underfull \hbox (badness 10000) in paragraph at lines 49557--49559 []|\T1/pcr/m/n/10 dihedral_- Underfull \hbox (badness 10000) in paragraph at lines 49573--49575 []|\T1/ptm/m/n/10 ori-en-ta-tion Overfull \hbox (14.50536pt too wide) in paragraph at lines 49576--49578 []|\T1/pcr/m/n/10 orientation_- Underfull \hbox (badness 10000) in paragraph at lines 49585--49587 \T1/ptm/m/n/10 (U); weight Underfull \hbox (badness 10000) in paragraph at lines 49592--49594 []|\T1/pcr/m/n/10 angle_- Underfull \hbox (badness 10000) in paragraph at lines 49608--49610 []|\T1/ptm/m/n/10 an-gle re-straint Underfull \hbox (badness 10000) in paragraph at lines 49611--49613 []|\T1/pcr/m/n/10 angle_- Overfull \hbox (8.50536pt too wide) in paragraph at lines 49611--49613 \T1/pcr/m/n/10 restraints_- [443] [444] [445 pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49653 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49653 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49653 \item { }] LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile1' on page 446 undefined on input line 49656. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile1' on page 446 undefined on input line 49656. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 446 undefined on input line 49661. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 446 undefined on input line 49661. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 446 u ndefined on input line 49721. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 446 undefin ed on input line 49721. [446] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 447 u ndefined on input line 49831. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 447 undefin ed on input line 49831. [447] LaTeX Warning: Hyper reference `reference-manual/topologies/parameter-files:nbp ar' on page 448 undefined on input line 49864. LaTeX Warning: Reference `reference-manual/topologies/parameter-files:nbpar' on page 448 undefined on input line 49864. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 448 und efined on input line 49889. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 448 undefined on input line 49889. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 448 undefined on input line 49911. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 448 undefi ned on input line 49911. LaTeX Warning: Hyper reference `reference-manual/references:refryckaert78' on p age 448 undefined on input line 49947. LaTeX Warning: Reference `reference-manual/references:refryckaert78' on page 44 8 undefined on input line 49947. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:positionr estraint' on page 448 undefined on input line 49956. LaTeX Warning: Reference `reference-manual/functions/restraints:positionrestrai nt' on page 448 undefined on input line 49956. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 448 u ndefined on input line 49957. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 448 undefin ed on input line 49957. [448] LaTeX Warning: Hyper reference `reference-manual/functions/restraints:dihedralr estraint' on page 449 undefined on input line 49962. LaTeX Warning: Reference `reference-manual/functions/restraints:dihedralrestrai nt' on page 449 undefined on input line 49962. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqndph i' on page 449 undefined on input line 49971. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqndih re' on page 449 undefined on input line 49972. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqndih re' on page 449 undefined on input line 49976. LaTeX Warning: Reference `equation:reference-manual/functions/restraints:eqndih re' on page 449 undefined on input line 49981. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:molitp' on page 449 undefined on input line 49988. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:mol itp' on page 449 undefined on input line 49988. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 449 undefined on input line 49995. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 449 undefi ned on input line 49995. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 449 u ndefined on input line 50000. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 449 undefin ed on input line 50000. LaTeX Warning: Hyper reference `onlinehelp/gmx-genion:gmx-genion' on page 449 u ndefined on input line 50002. LaTeX Warning: Reference `onlinehelp/gmx-genion:gmx-genion' on page 449 undefin ed on input line 50002. LaTeX Warning: Hyper reference `reference-manual/algorithms/group-concept:group concept' on page 449 undefined on input line 50004. LaTeX Warning: Reference `reference-manual/algorithms/group-concept:groupconcep t' on page 449 undefined on input line 50004. LaTeX Warning: Hyper reference `reference-manual/analysis/using-groups:usinggro ups' on page 449 undefined on input line 50005. LaTeX Warning: Reference `reference-manual/analysis/using-groups:usinggroups' o n page 449 undefined on input line 50005. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 449 undefined on input line 50016. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 449 undef ined on input line 50016. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 449 undefined on input line 50045. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 449 undefi ned on input line 50045. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 449 undefined on input line 50046. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 449 undefi ned on input line 50046. [449] LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 450 undefined on input line 50074. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 450 undefi ned on input line 50074. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 450 undefined on input line 50078. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 450 undefi ned on input line 50078. LaTeX Warning: Hyper reference `reference-manual/references:refloof92' on page 450 undefined on input line 50080. LaTeX Warning: Reference `reference-manual/references:refloof92' on page 450 un defined on input line 50080. LaTeX Warning: Hyper reference `reference-manual/references:refbuuren93a' on pa ge 450 undefined on input line 50081. LaTeX Warning: Reference `reference-manual/references:refbuuren93a' on page 450 undefined on input line 50081. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 450 u ndefined on input line 50083. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 450 undefin ed on input line 50083. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 450 undefined on input line 50090. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 450 undefi ned on input line 50090. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 450 u ndefined on input line 50090. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 450 undefin ed on input line 50090. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 450 undefined on input line 50092. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 450 undefi ned on input line 50092. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 450 undefined on input line 50092. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 450 undefi ned on input line 50092. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 450 undefined on input line 50097. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 450 undefi ned on input line 50097. [450] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 451 undefined on input line 50140. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 451 undef ined on input line 50140. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:positionr estraint' on page 451 undefined on input line 50141. LaTeX Warning: Reference `reference-manual/functions/restraints:positionrestrai nt' on page 451 undefined on input line 50141. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 451 undefined on input line 50141. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 451 undefi ned on input line 50141. LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fecalc' on page 451 undefined on input line 50150. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fecalc' on page 451 undefined on input line 50150. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile1' on page 451 undefined on input line 50156. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile1' on page 451 undefined on input line 50156. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfile2' on page 451 undefined on input line 50156. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfile2' on page 451 undefined on input line 50156. LaTeX Warning: Hyper reference `reference-manual/functions/free-energy-interact ions:feia' on page 451 undefined on input line 50158. LaTeX Warning: Reference `reference-manual/functions/free-energy-interactions:f eia' on page 451 undefined on input line 50158. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:tab-topfe' on page 451 undefined on input line 50161. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:tab -topfe' on page 451 undefined on input line 50161. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 451 u ndefined on input line 50164. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 451 undefin ed on input line 50164. Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50222--50225 []\T1/phv/m/n/10 ex-pected Underfull \hbox (badness 10000) detected at line 50226 []\T1/phv/m/n/10 ex-pected [451] [452] LaTeX Warning: Hyper reference `reference-manual/special/pulling:pull' on page 453 undefined on input line 50592. LaTeX Warning: Reference `reference-manual/special/pulling:pull' on page 453 un defined on input line 50592. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :excl' on page 453 undefined on input line 50600. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:excl' on page 453 undefined on input line 50600. [453] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 454 undefined on input line 50641. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 454 undefi ned on input line 50641. [454] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 455 undefined on input line 50703. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 455 undef ined on input line 50703. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 455 undefined on input line 50783. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 455 undefined on input line 50783. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 455 undefined on input line 50787. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 455 undef ined on input line 50787. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 455 undefined on input line 50788. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 455 undefi ned on input line 50788. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 455 undefined on input line 50789. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 455 undefi ned on input line 50789. LaTeX Warning: Hyper reference `reference-manual/file-formats:atp' on page 455 undefined on input line 50792. LaTeX Warning: Reference `reference-manual/file-formats:atp' on page 455 undefi ned on input line 50792. LaTeX Warning: Hyper reference `reference-manual/topologies/pdb2gmx-input-files :pdb2gmxfiles' on page 455 undefined on input line 50793. LaTeX Warning: Reference `reference-manual/topologies/pdb2gmx-input-files:pdb2g mxfiles' on page 455 undefined on input line 50793. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 455 undefined on input line 50802. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 455 undefi ned on input line 50802. LaTeX Warning: Hyper reference `reference-manual/topologies/topology-file-forma ts:topfile' on page 455 undefined on input line 50803. LaTeX Warning: Reference `reference-manual/topologies/topology-file-formats:top file' on page 455 undefined on input line 50803. [455] [456] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 457 undefined on input line 50846. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 457 undefi ned on input line 50846. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 457 u ndefined on input line 50847. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 457 undefin ed on input line 50847. LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 457 undefined on input line 50847. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 4 57 undefined on input line 50847. LaTeX Warning: Hyper reference `reference-manual/file-formats:m2p' on page 457 undefined on input line 50850. LaTeX Warning: Reference `reference-manual/file-formats:m2p' on page 457 undefi ned on input line 50850. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 457 u ndefined on input line 50851. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 457 undefin ed on input line 50851. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 457 undefined on input line 50859. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 457 undefi ned on input line 50859. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 457 undefined on input line 50863. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 457 undefi ned on input line 50863. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 457 undefined on input line 50867. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 457 undefi ned on input line 50867. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 457 undefined on input line 50871. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 457 undefi ned on input line 50871. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 457 undefined on input line 50871. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 457 undefi ned on input line 50871. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 457 undefined on input line 50871. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 457 undefi ned on input line 50871. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 457 undefined on input line 50871. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 457 undefi ned on input line 50871. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 457 undefined on input line 50881. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 457 undefi ned on input line 50881. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 457 undefined on input line 50885. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 457 undefi ned on input line 50885. LaTeX Warning: Hyper reference `reference-manual/file-formats:rtp' on page 457 undefined on input line 50889. LaTeX Warning: Reference `reference-manual/file-formats:rtp' on page 457 undefi ned on input line 50889. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 457 undefined on input line 50893. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 457 undefi ned on input line 50893. LaTeX Warning: Hyper reference `reference-manual/file-formats:n2t' on page 457 undefined on input line 50897. LaTeX Warning: Reference `reference-manual/file-formats:n2t' on page 457 undefi ned on input line 50897. LaTeX Warning: Hyper reference `reference-manual/file-formats:atp' on page 457 undefined on input line 50901. LaTeX Warning: Reference `reference-manual/file-formats:atp' on page 457 undefi ned on input line 50901. LaTeX Warning: Hyper reference `reference-manual/file-formats:r2b' on page 457 undefined on input line 50905. LaTeX Warning: Reference `reference-manual/file-formats:r2b' on page 457 undefi ned on input line 50905. LaTeX Warning: Hyper reference `reference-manual/file-formats:arn' on page 457 undefined on input line 50909. LaTeX Warning: Reference `reference-manual/file-formats:arn' on page 457 undefi ned on input line 50909. LaTeX Warning: Hyper reference `reference-manual/file-formats:hdb' on page 457 undefined on input line 50913. LaTeX Warning: Reference `reference-manual/file-formats:hdb' on page 457 undefi ned on input line 50913. LaTeX Warning: Hyper reference `reference-manual/file-formats:vsd' on page 457 undefined on input line 50917. LaTeX Warning: Reference `reference-manual/file-formats:vsd' on page 457 undefi ned on input line 50917. LaTeX Warning: Hyper reference `reference-manual/file-formats:tdb' on page 457 undefined on input line 50921. LaTeX Warning: Reference `reference-manual/file-formats:tdb' on page 457 undefi ned on input line 50921. [457] LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 458 undefined on input line 50930. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 458 undefi ned on input line 50930. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 458 undefined on input line 50939. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 458 undefi ned on input line 50939. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 458 undefined on input line 50943. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 458 undefi ned on input line 50943. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 458 undefined on input line 50947. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 458 undefi ned on input line 50947. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 458 undefined on input line 50951. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 458 undefi ned on input line 50951. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 458 undefined on input line 50955. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 458 undefi ned on input line 50955. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 458 undefined on input line 50959. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 458 undefi ned on input line 50959. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 458 undefined on input line 50964. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 458 undefi ned on input line 50964. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 458 undefined on input line 50964. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 458 undefi ned on input line 50964. LaTeX Warning: Hyper reference `reference-manual/file-formats:tng' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:tng' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:xtc' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:xtc' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:g96' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:g96' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 458 undefined on input line 50968. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 458 undefi ned on input line 50968. LaTeX Warning: Hyper reference `reference-manual/file-formats:ene' on page 458 undefined on input line 50976. LaTeX Warning: Reference `reference-manual/file-formats:ene' on page 458 undefi ned on input line 50976. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 458 undefined on input line 50980. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 458 undefi ned on input line 50980. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 458 undefined on input line 50985. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 458 undefi ned on input line 50985. LaTeX Warning: Hyper reference `reference-manual/file-formats:ene' on page 458 undefined on input line 50985. LaTeX Warning: Reference `reference-manual/file-formats:ene' on page 458 undefi ned on input line 50985. LaTeX Warning: Hyper reference `reference-manual/file-formats:dat' on page 458 undefined on input line 50993. LaTeX Warning: Reference `reference-manual/file-formats:dat' on page 458 undefi ned on input line 50993. LaTeX Warning: Hyper reference `reference-manual/file-formats:edi' on page 458 undefined on input line 50997. LaTeX Warning: Reference `reference-manual/file-formats:edi' on page 458 undefi ned on input line 50997. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 458 und efined on input line 50998. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 458 undefined on input line 50998. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 458 undefined on input line 51001. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 458 undefi ned on input line 51001. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 458 undefined on input line 51005. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 458 undefi ned on input line 51005. LaTeX Warning: Hyper reference `reference-manual/file-formats:mtx' on page 458 undefined on input line 51009. LaTeX Warning: Reference `reference-manual/file-formats:mtx' on page 458 undefi ned on input line 51009. LaTeX Warning: Hyper reference `reference-manual/file-formats:out' on page 458 undefined on input line 51013. LaTeX Warning: Reference `reference-manual/file-formats:out' on page 458 undefi ned on input line 51013. LaTeX Warning: Hyper reference `reference-manual/file-formats:tex' on page 458 undefined on input line 51017. LaTeX Warning: Reference `reference-manual/file-formats:tex' on page 458 undefi ned on input line 51017. LaTeX Warning: Hyper reference `reference-manual/file-formats:xpm' on page 458 undefined on input line 51021. LaTeX Warning: Reference `reference-manual/file-formats:xpm' on page 458 undefi ned on input line 51021. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 458 u ndefined on input line 51022. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 458 undefin ed on input line 51022. LaTeX Warning: Hyper reference `reference-manual/file-formats:eps' on page 458 undefined on input line 51022. LaTeX Warning: Reference `reference-manual/file-formats:eps' on page 458 undefi ned on input line 51022. LaTeX Warning: Hyper reference `reference-manual/file-formats:xvg' on page 458 undefined on input line 51025. LaTeX Warning: Reference `reference-manual/file-formats:xvg' on page 458 undefi ned on input line 51025. [458] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 und efined on input line 51059. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 undefined on input line 51059. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 und efined on input line 51074. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 undefined on input line 51074. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 459 u ndefined on input line 51087. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 459 undefin ed on input line 51087. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 und efined on input line 51094. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 459 undefined on input line 51094. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 459 undefined on input line 51098. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 459 undefi ned on input line 51098. LaTeX Warning: Hyper reference `onlinehelp/gmx-eneconv:gmx-eneconv' on page 459 undefined on input line 51099. LaTeX Warning: Reference `onlinehelp/gmx-eneconv:gmx-eneconv' on page 459 undef ined on input line 51099. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 459 u ndefined on input line 51102. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 459 undefin ed on input line 51102. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 459 u ndefined on input line 51110. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 459 undefin ed on input line 51110. [459 <./plotje.png>] [460] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 461 undefined on input line 51280. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 461 undef ined on input line 51280. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 461 undefined on input line 51289. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 461 undefi ned on input line 51289. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 461 u ndefined on input line 51303. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 461 undefin ed on input line 51303. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 461 u ndefined on input line 51305. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 461 undefin ed on input line 51305. [461] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 462 u ndefined on input line 51355. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 462 undefin ed on input line 51355. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 462 u ndefined on input line 51400. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 462 undefin ed on input line 51400. [462] LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 463 undefined on input line 51414. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 463 undefi ned on input line 51414. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 463 und efined on input line 51416. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 463 undefined on input line 51416. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 463 und efined on input line 51417. LaTeX Warning: Reference `onlinehelp/gmx-nmeig:gmx-nmeig' on page 463 undefined on input line 51417. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 463 u ndefined on input line 51425. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 463 undefin ed on input line 51425. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 4 63 undefined on input line 51453. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 463 und efined on input line 51453. LaTeX Warning: Hyper reference `onlinehelp/gmx-x2top:gmx-x2top' on page 463 und efined on input line 51461. LaTeX Warning: Reference `onlinehelp/gmx-x2top:gmx-x2top' on page 463 undefined on input line 51461. [463] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 464 undefined on input line 51520. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 464 undefi ned on input line 51520. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undefined on input line 51551. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undef ined on input line 51551. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 464 undefined on input line 51552. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 464 undefi ned on input line 51552. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 464 undefined on input line 51557. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 464 undefi ned on input line 51557. LaTeX Warning: Hyper reference `reference-manual/file-formats:top' on page 464 undefined on input line 51560. LaTeX Warning: Reference `reference-manual/file-formats:top' on page 464 undefi ned on input line 51560. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undefined on input line 51564. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undef ined on input line 51564. LaTeX Warning: Hyper reference `reference-manual/file-formats:itp' on page 464 undefined on input line 51566. LaTeX Warning: Reference `reference-manual/file-formats:itp' on page 464 undefi ned on input line 51566. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undefined on input line 51569. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undef ined on input line 51569. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undefined on input line 51576. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 464 undef ined on input line 51576. [464] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 465 undefined on input line 51677. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 465 undefi ned on input line 51677. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 465 und efined on input line 51678. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 465 undefined on input line 51678. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 465 undef ined on input line 51680. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 465 undefined o n input line 51680. LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 465 undef ined on input line 51682. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 465 undefined o n input line 51682. [465] LaTeX Warning: Hyper reference `onlinehelp/gmx-check:gmx-check' on page 466 und efined on input line 51696. LaTeX Warning: Reference `onlinehelp/gmx-check:gmx-check' on page 466 undefined on input line 51696. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 466 u ndefined on input line 51704. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 466 undefin ed on input line 51704. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 466 undefined on input line 51705. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 466 undefi ned on input line 51705. [466] LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 467 undef ined on input line 51807. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 467 undefined o n input line 51807. LaTeX Warning: Hyper reference `onlinehelp/gmx-check:gmx-check' on page 467 und efined on input line 51820. LaTeX Warning: Reference `onlinehelp/gmx-check:gmx-check' on page 467 undefined on input line 51820. [467] LaTeX Warning: Hyper reference `onlinehelp/gmx-dump:gmx-dump' on page 468 undef ined on input line 51830. LaTeX Warning: Reference `onlinehelp/gmx-dump:gmx-dump' on page 468 undefined o n input line 51830. LaTeX Warning: Hyper reference `onlinehelp/gmx-check:gmx-check' on page 468 und efined on input line 51847. LaTeX Warning: Reference `onlinehelp/gmx-check:gmx-check' on page 468 undefined on input line 51847. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 468 u ndefined on input line 51876. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 468 undefin ed on input line 51876. [468] [469] [470 <./xvgr.png>] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 471 undefined on input line 52075. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 471 undefi ned on input line 52075. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 471 undefined on input line 52079. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 471 undefi ned on input line 52079. LaTeX Warning: Hyper reference `reference-manual/special/free-energy-implementa tion:figlambdaval' on page 471 undefined on input line 52119. LaTeX Warning: Reference `reference-manual/special/free-energy-implementation:f iglambdaval' on page 471 undefined on input line 52119. [471 <./lambda-values.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refrmneumann1980a' on page 472 undefined on input line 52225. LaTeX Warning: Reference `reference-manual/references:refrmneumann1980a' on pag e 472 undefined on input line 52225. [472] LaTeX Warning: Hyper reference `reference-manual/references:refjarzynski1997a' on page 473 undefined on input line 52253. LaTeX Warning: Reference `reference-manual/references:refjarzynski1997a' on pag e 473 undefined on input line 52253. LaTeX Warning: Hyper reference `reference-manual/special/pulling:transformation coord' on page 473 undefined on input line 52272. LaTeX Warning: Reference `reference-manual/special/pulling:transformationcoord' on page 473 undefined on input line 52272. LaTeX Warning: Hyper reference `reference-manual/special/awh::doc' on page 473 undefined on input line 52330. LaTeX Warning: Reference `reference-manual/special/awh::doc' on page 473 undefi ned on input line 52330. [473 <./pull.pdf>] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 474 undefined on input line 52337. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 474 undefi ned on input line 52337. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 474 undefined on input line 52371. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 474 undefi ned on input line 52371. LaTeX Warning: Hyper reference `reference-manual/references:refengin2010a' on p age 474 undefined on input line 52429. LaTeX Warning: Reference `reference-manual/references:refengin2010a' on page 47 4 undefined on input line 52429. [474] LaTeX Warning: Hyper reference `reference-manual/special/pulling:fig-pulldirrel ' on page 475 undefined on input line 52474. LaTeX Warning: Reference `reference-manual/special/pulling:fig-pulldirrel' on p age 475 undefined on input line 52474. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 475 undefined on input line 52500. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 475 undefi ned on input line 52500. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 475 undefined on input line 52514. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 475 undefi ned on input line 52514. [475 <./pullref.pdf>] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 476 undefined on input line 52548. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 476 undefi ned on input line 52548. [476 <./pulldirrel.pdf>] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 477 undefined on input line 52615. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 477 undefi ned on input line 52615. LaTeX Warning: Hyper reference `reference-manual/special/free-energy-pmf:fepmf' on page 477 undefined on input line 52618. LaTeX Warning: Reference `reference-manual/special/free-energy-pmf:fepmf' on pa ge 477 undefined on input line 52618. [477] LaTeX Warning: Hyper reference `reference-manual/references:reflidmar2012' on p age 478 undefined on input line 52630. LaTeX Warning: Reference `reference-manual/references:reflidmar2012' on page 47 8 undefined on input line 52630. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 478 undefined on input line 52631. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 478 undefined on input line 52631. LaTeX Warning: Hyper reference `reference-manual/references:refwang2001efficien t' on page 478 undefined on input line 52636. LaTeX Warning: Reference `reference-manual/references:refwang2001efficient' on page 478 undefined on input line 52636. LaTeX Warning: Hyper reference `reference-manual/references:refhuber1994local' on page 478 undefined on input line 52637. LaTeX Warning: Reference `reference-manual/references:refhuber1994local' on pag e 478 undefined on input line 52637. LaTeX Warning: Hyper reference `reference-manual/references:reflaio2002escaping ' on page 478 undefined on input line 52638. LaTeX Warning: Reference `reference-manual/references:reflaio2002escaping' on p age 478 undefined on input line 52638. LaTeX Warning: Hyper reference `reference-manual/references:reflundborg2021' on page 478 undefined on input line 52649. LaTeX Warning: Reference `reference-manual/references:reflundborg2021' on page 478 undefined on input line 52649. LaTeX Warning: Hyper reference `reference-manual/references:reflyubartsev1992' on page 478 undefined on input line 52656. LaTeX Warning: Reference `reference-manual/references:reflyubartsev1992' on pag e 478 undefined on input line 52656. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhplambda' o n page 478 undefined on input line 52692. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhplambda' o n page 478 undefined on input line 52721. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhtargets' on pag e 478 undefined on input line 52723. LaTeX Warning: Reference `reference-manual/special/awh:awhtargets' on page 478 undefined on input line 52723. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhplambda' o n page 478 undefined on input line 52724. [478] LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhdfnaive' o n page 479 undefined on input line 52744. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhinitialstage' o n page 479 undefined on input line 52753. LaTeX Warning: Reference `reference-manual/special/awh:awhinitialstage' on page 479 undefined on input line 52753. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhgrhofrelat ion' on page 479 undefined on input line 52763. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhplambda' o n page 479 undefined on input line 52766. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqnawhbasic' on page 479 undefined on input line 52771. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 479 undefined on input line 52774. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 479 undefined on input line 52774. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 479 undefined on input line 52792. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 479 undefined on input line 52792. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhreweight' on pa ge 479 undefined on input line 52793. LaTeX Warning: Reference `reference-manual/special/awh:awhreweight' on page 479 undefined on input line 52793. LaTeX Warning: Hyper reference `reference-manual/special/awh:fig-awhbiasevoluti on1' on page 479 undefined on input line 52794. LaTeX Warning: Reference `reference-manual/special/awh:fig-awhbiasevolution1' o n page 479 undefined on input line 52794. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhusage' on page 479 undefined on input line 52795. LaTeX Warning: Reference `reference-manual/special/awh:awhusage' on page 479 un defined on input line 52795. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhomega' on page 479 undefined on input line 52805. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhpxlambda' on page 479 undefined on input line 52814. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhwupdate' o n page 479 undefined on input line 52876. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhwupdate' o n page 479 undefined on input line 52881. LaTeX Warning: Hyper reference `reference-manual/references:refwang2001efficien t' on page 479 undefined on input line 52882. LaTeX Warning: Reference `reference-manual/references:refwang2001efficient' on page 479 undefined on input line 52882. [479] [480 <./awh-traj.pdf> <./awh-invN.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-invN.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [481 <./awh-sampleweights.pdf> <./awh-pmfs.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-pmfs.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhcovering' on page 482 undefined on input line 52889. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhdfsize' on page 482 undefined on input line 52895. LaTeX Warning: Hyper reference `reference-manual/special/awh:fig-awhbiasevoluti on1' on page 482 undefined on input line 52897. LaTeX Warning: Reference `reference-manual/special/awh:fig-awhbiasevolution1' o n page 482 undefined on input line 52897. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhgrhofrelat ion' on page 482 undefined on input line 52902. LaTeX Warning: Hyper reference `reference-manual/special/awh:fig-awhbiasevoluti on1' on page 482 undefined on input line 52912. LaTeX Warning: Reference `reference-manual/special/awh:fig-awhbiasevolution1' o n page 482 undefined on input line 52912. LaTeX Warning: Hyper reference `reference-manual/references:refbelardinelli2007 fast' on page 482 undefined on input line 52947. LaTeX Warning: Reference `reference-manual/references:refbelardinelli2007fast' on page 482 undefined on input line 52947. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 482 undefined on input line 52952. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 482 undefined on input line 52952. LaTeX Warning: Hyper reference `reference-manual/special/awh:fig-awhbiasevoluti on1' on page 482 undefined on input line 52963. LaTeX Warning: Reference `reference-manual/special/awh:fig-awhbiasevolution1' o n page 482 undefined on input line 52963. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhwupdate' o n page 482 undefined on input line 52987. [482] LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhgrhofrelat ion' on page 483 undefined on input line 53031. LaTeX Warning: Hyper reference `reference-manual/references:refbarducci2008well ' on page 483 undefined on input line 53040. LaTeX Warning: Reference `reference-manual/references:refbarducci2008well' on p age 483 undefined on input line 53040. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 483 undefined on input line 53041. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 483 undefined on input line 53041. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhwupdate' o n page 483 undefined on input line 53050. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhinitialstage' o n page 483 undefined on input line 53066. LaTeX Warning: Reference `reference-manual/special/awh:awhinitialstage' on page 483 undefined on input line 53066. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhfriction' on pa ge 483 undefined on input line 53085. LaTeX Warning: Reference `reference-manual/special/awh:awhfriction' on page 483 undefined on input line 53085. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhsqrtmetric ' on page 483 undefined on input line 53087. [483] LaTeX Warning: Hyper reference `reference-manual/special/awh:awhinitialstage' o n page 484 undefined on input line 53100. LaTeX Warning: Reference `reference-manual/special/awh:awhinitialstage' on page 484 undefined on input line 53100. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-target-metric-s caling-limit' on page 484 undefined on input line 53113. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-target-metric-scaling -limit' on page 484 undefined on input line 53113. LaTeX Warning: Hyper reference `reference-manual/references:reflundborg2023' on page 484 undefined on input line 53117. LaTeX Warning: Reference `reference-manual/references:reflundborg2023' on page 484 undefined on input line 53117. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhinitialstage' o n page 484 undefined on input line 53141. LaTeX Warning: Reference `reference-manual/special/awh:awhinitialstage' on page 484 undefined on input line 53141. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhcovering' on page 484 undefined on input line 53168. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhcovering' on page 484 undefined on input line 53179. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh-share-multisim' on page 484 undefined on input line 53187. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh-share-multisim' on pag e 484 undefined on input line 53187. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-awh1-share-group' on page 484 undefined on input line 53188. LaTeX Warning: Reference `user-guide/mdp-options:mdp-awh1-share-group' on page 484 undefined on input line 53188. [484] LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhbiaspotent ial' on page 485 undefined on input line 53206. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhunbias' on page 485 undefined on input line 53229. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhunbias' on page 485 undefined on input line 53235. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2017seque nce' on page 485 undefined on input line 53236. LaTeX Warning: Reference `reference-manual/references:reflindahl2017sequence' o n page 485 undefined on input line 53236. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhomega' on page 485 undefined on input line 53262. LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2018' on page 485 undefined on input line 53264. LaTeX Warning: Reference `reference-manual/references:reflindahl2018' on page 4 85 undefined on input line 53264. LaTeX Warning: Hyper reference `reference-manual/references:refsivak2012thermod ynamic' on page 485 undefined on input line 53264. LaTeX Warning: Reference `reference-manual/references:refsivak2012thermodynamic ' on page 485 undefined on input line 53264. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 485 undefined on input line 53299. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 485 undefi ned on input line 53299. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 485 undefin ed on input line 53302. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 485 undefined on input line 53302. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 485 undefined on input line 53304. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 485 undefi ned on input line 53304. [485] LaTeX Warning: Hyper reference `reference-manual/references:reflindahl2014accel erated' on page 486 undefined on input line 53316. LaTeX Warning: Reference `reference-manual/references:reflindahl2014accelerated ' on page 486 undefined on input line 53316. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 486 undefin ed on input line 53348. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 486 undefined on input line 53348. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhrhocut' on page 486 undefined on input line 53396. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhreweight' on pa ge 486 undefined on input line 53404. LaTeX Warning: Reference `reference-manual/special/awh:awhreweight' on page 486 undefined on input line 53404. LaTeX Warning: Hyper reference `reference-manual/special/awh:awhfriction' on pa ge 486 undefined on input line 53413. LaTeX Warning: Reference `reference-manual/special/awh:awhfriction' on page 486 undefined on input line 53413. LaTeX Warning: Reference `equation:reference-manual/special/awh:eqawhsqrtmetric ' on page 486 undefined on input line 53415. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 486 undefin ed on input line 53416. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 486 undefined on input line 53416. [486] LaTeX Warning: Hyper reference `reference-manual/references:refkutzner2011' on page 487 undefined on input line 53431. LaTeX Warning: Reference `reference-manual/references:refkutzner2011' on page 4 87 undefined on input line 53431. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- rotation' on page 487 undefined on input line 53481. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-rotati on' on page 487 undefined on input line 53481. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 487 undefined on input line 53517. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 487 undefined on input line 53517. [487 <./rotation.pdf>] [488 <./equipotential.pdf>] LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotiso' on page 489 undefined on input line 53569. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotisopf' on page 489 undefined on input line 53569. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotpm' on page 489 undefined on input line 53611. [489 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53629 \subsubsection{Radial Motion Potential} ] LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 490 undefined on input line 53640. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 490 undefined on input line 53640. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 490 undefined on input line 53696. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 490 undefined on input line 53696. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 490 undefined on input line 53701. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 490 undefined on input line 53701. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 490 undefined on input line 53723. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 490 undefined on input line 53723. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2' on page 490 undefined on input line 53724. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 490 undefined on input line 53727. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 490 undefined on input line 53727. [490] LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- rotation' on page 491 undefined on input line 53799. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-rotati on' on page 491 undefined on input line 53799. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrmpf' on page 491 undefined on input line 53804. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2pf' on page 491 undefined on input line 53804. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- rotation' on page 491 undefined on input line 53806. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-rotati on' on page 491 undefined on input line 53806. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- rotation' on page 491 undefined on input line 53810. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-rotati on' on page 491 undefined on input line 53810. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- gaussian' on page 491 undefined on input line 53849. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-gaussi an' on page 491 undefined on input line 53849. [491 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.35 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53881 \end{equation} ] LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrmpf' on page 492 undefined on input line 53894. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 492 undefined on input line 53894. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 492 undefined on input line 53894. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrmpf' on page 492 undefined on input line 53912. [492 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53968 \end{equation} <./gaussians.pdf>] LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflexforce' on page 493 undefined on input line 53977. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2pf' on page 493 undefined on input line 53984. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:fig- equipotential' on page 493 undefined on input line 53986. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:fig-equipo tential' on page 493 undefined on input line 53986. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qntrafo' on page 493 undefined on input line 54040. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 493 undefined on input line 54058. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 493 undefi ned on input line 54058. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 493 undefined on input line 54060. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 493 undefi ned on input line 54060. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 493 u ndefined on input line 54060. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 493 undefin ed on input line 54060. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 493 undefined on input line 54062. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 493 undefi ned on input line 54062. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:tab- vars' on page 493 undefined on input line 54065. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:tab-vars' on page 493 undefined on input line 54065. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 493 undefined on input line 54065. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 493 undefi ned on input line 54065. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:tab- quantities' on page 493 undefined on input line 54073. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:tab-quanti ties' on page 493 undefined on input line 54073. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 493 undefined on input line 54578. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 493 undefi ned on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotiso' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotisopf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotpm' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotpmpf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrmpf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2pf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflex' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflext' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflex2' on page 493 undefined on input line 54578. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 493 undefined on input line 54578. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 493 undefi ned on input line 54578. Overfull \hbox (1.16202pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 pivot| Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 slab- Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 min- Overfull \hbox (1.80867pt too wide) in paragraph at lines 54578--54578 []$[]$| Overfull \hbox (0.99873pt too wide) in paragraph at lines 54578--54578 []$[]$\T1/phv/m/n/10 /ps| Overfull \hbox (1.02318pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 nm$[]$| LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotiso' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotisopf' on page 493 undefined on input line 54578. Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/ptm/m/n/10 par-al-lel mo- LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotpm' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotpmpf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrmpf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotrm2pf' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflex' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflext' on page 493 undefined on input line 54578. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnpotflex2' on page 493 undefined on input line 54578. [493] LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:tab- vars' on page 494 undefined on input line 54751. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:tab-vars' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnavangle' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnrmsdfit' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qndefx0' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qndefy0' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qntorque' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qntorque' on page 494 undefined on input line 54751. LaTeX Warning: Hyper reference `reference-manual/special/enforced-rotation:tab- vars' on page 494 undefined on input line 54751. LaTeX Warning: Reference `reference-manual/special/enforced-rotation:tab-vars' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnavangle' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnrmsdfit' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qndefx0' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qndefy0' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qntorque' on page 494 undefined on input line 54751. LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qntorque' on page 494 undefined on input line 54751. pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnproject' on page 494 undefined on input line 54771. [494] LaTeX Warning: Reference `equation:reference-manual/special/enforced-rotation:e qnrmsdfit' on page 495 undefined on input line 54804. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 495 undefined on input line 54808. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 495 undefi ned on input line 54808. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-electric-field-x' on page 495 undefined on input line 54864. LaTeX Warning: Reference `user-guide/mdp-options:mdp-electric-field-x' on page 495 undefined on input line 54864. LaTeX Warning: Hyper reference `reference-manual/references:refcaleman2008a' on page 495 undefined on input line 54868. LaTeX Warning: Reference `reference-manual/references:refcaleman2008a' on page 495 undefined on input line 54868. LaTeX Warning: Hyper reference `reference-manual/special/electric-fields:fig-fi eld' on page 495 undefined on input line 54869. LaTeX Warning: Reference `reference-manual/special/electric-fields:fig-field' o n page 495 undefined on input line 54869. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:compe l' on page 495 undefined on input line 54879. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:compel' on page 495 undefined on input line 54879. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 495 u ndefined on input line 54890. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 495 undefin ed on input line 54890. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 495 undefined on input line 54890. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 495 undefi ned on input line 54890. [495] LaTeX Warning: Hyper reference `reference-manual/references:refcaleman2008a' on page 496 undefined on input line 54916. LaTeX Warning: Reference `reference-manual/references:refcaleman2008a' on page 496 undefined on input line 54916. LaTeX Warning: Hyper reference `reference-manual/special/electric-fields:fig-fi eld' on page 496 undefined on input line 54918. LaTeX Warning: Reference `reference-manual/special/electric-fields:fig-field' o n page 496 undefined on input line 54918. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 496 und efined on input line 54919. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 496 undefined on input line 54919. [496 <./field.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refkutzner2011b' on page 497 undefined on input line 54980. LaTeX Warning: Reference `reference-manual/references:refkutzner2011b' on page 497 undefined on input line 54980. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 497 undefined on input line 54991. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 497 undefi ned on input line 54991. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:fig-c ompelsetup' on page 497 undefined on input line 55006. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:fig-compels etup' on page 497 undefined on input line 55006. LaTeX Warning: Hyper reference `onlinehelp/gmx-potential:gmx-potential' on page 497 undefined on input line 55025. LaTeX Warning: Reference `onlinehelp/gmx-potential:gmx-potential' on page 497 u ndefined on input line 55025. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:fig-c ompelsetup' on page 497 undefined on input line 55027. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:fig-compels etup' on page 497 undefined on input line 55027. [497 <./compelsetup.pdf>] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 498 undefined on input line 55055. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 498 undefi ned on input line 55055. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:fig-c ompelsetup' on page 498 undefined on input line 55064. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:fig-compels etup' on page 498 undefined on input line 55064. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:fig-c ompelsetup' on page 498 undefined on input line 55090. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:fig-compels etup' on page 498 undefined on input line 55090. LaTeX Warning: Hyper reference `reference-manual/special/comp-electrophys:fig-c ompelsetup' on page 498 undefined on input line 55107. LaTeX Warning: Reference `reference-manual/special/comp-electrophys:fig-compels etup' on page 498 undefined on input line 55107. [498] LaTeX Warning: Hyper reference `onlinehelp/gmx-editconf:gmx-editconf' on page 4 99 undefined on input line 55185. LaTeX Warning: Reference `onlinehelp/gmx-editconf:gmx-editconf' on page 499 und efined on input line 55185. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 4 99 undefined on input line 55187. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 499 und efined on input line 55187. LaTeX Warning: Hyper reference `reference-manual/special/pulling:pull' on page 499 undefined on input line 55195. LaTeX Warning: Reference `reference-manual/special/pulling:pull' on page 499 un defined on input line 55195. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 499 undefined on input line 55204. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 499 undefi ned on input line 55204. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 499 undefined on input line 55211. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 499 undefi ned on input line 55211. LaTeX Warning: Hyper reference `reference-manual/algorithms/free-energy-calcula tions:fecalc' on page 499 undefined on input line 55221. LaTeX Warning: Reference `reference-manual/algorithms/free-energy-calculations: fecalc' on page 499 undefined on input line 55221. LaTeX Warning: Hyper reference `reference-manual/topologies/molecule-definition :excl' on page 499 undefined on input line 55226. LaTeX Warning: Reference `reference-manual/topologies/molecule-definition:excl' on page 499 undefined on input line 55226. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 499 undefined on input line 55230. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 499 undefi ned on input line 55230. LaTeX Warning: Hyper reference `reference-manual/functions/restraints:positionr estraint' on page 499 undefined on input line 55239. LaTeX Warning: Reference `reference-manual/functions/restraints:positionrestrai nt' on page 499 undefined on input line 55239. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 499 u ndefined on input line 55242. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 499 undefin ed on input line 55242. [499] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: virtualsites' on page 500 undefined on input line 55287. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:virtua lsites' on page 500 undefined on input line 55287. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:vsiteh ydro' on page 500 undefined on input line 55296. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:vsitehydro' on page 500 undefined on input line 55296. LaTeX Warning: Hyper reference `reference-manual/references:reffeenstra99' on p age 500 undefined on input line 55297. LaTeX Warning: Reference `reference-manual/references:reffeenstra99' on page 50 0 undefined on input line 55297. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 500 undefined on input line 55311. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 500 undef ined on input line 55311. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 500 u ndefined on input line 55322. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 500 undefin ed on input line 55322. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 500 undefined on input line 55325. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 500 undef ined on input line 55325. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 500 undefined on input line 55366. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 500 undefined on input line 55366. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 500 undefined on input line 55374. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 500 undefined on input line 55374. [500] LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 501 undefined on input line 55390. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 501 undefined on input line 55390. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 501 undefined on input line 55400. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 501 undefined on input line 55400. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 501 undefined on input line 55419. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 501 undefined on input line 55419. [501 <./dumtypes.pdf> <./dumaro.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dumaro.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `reference-manual/functions/interaction-methods: virtualsites' on page 502 undefined on input line 55446. LaTeX Warning: Reference `reference-manual/functions/interaction-methods:virtua lsites' on page 502 undefined on input line 55446. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 502 undefined on input line 55455. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 502 undefined on input line 55455. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 502 undefined on input line 55471. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 502 undefined on input line 55471. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 502 undefined on input line 55482. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 502 undefined on input line 55482. LaTeX Warning: Hyper reference `reference-manual/special/remove-fast-dgf:fig-vs itehydro' on page 502 undefined on input line 55490. LaTeX Warning: Reference `reference-manual/special/remove-fast-dgf:fig-vsitehyd ro' on page 502 undefined on input line 55490. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 502 u ndefined on input line 55517. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 502 undefin ed on input line 55517. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002a' on pa ge 502 undefined on input line 55518. LaTeX Warning: Reference `reference-manual/references:refhess2002a' on page 502 undefined on input line 55518. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 502 und efined on input line 55524. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 502 undefined on input line 55524. [502] LaTeX Warning: Hyper reference `reference-manual/references:refberendsen91' on page 503 undefined on input line 55607. LaTeX Warning: Reference `reference-manual/references:refberendsen91' on page 5 03 undefined on input line 55607. LaTeX Warning: Reference `equation:reference-manual/special/viscosity-calculati on:eqnvisc' on page 503 undefined on input line 55629. [503] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 504 undefined on input line 55653. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 504 undefi ned on input line 55653. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 504 und efined on input line 55657. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 504 undefined on input line 55657. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 504 undefined on input line 55665. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 504 undefi ned on input line 55665. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 504 u ndefined on input line 55682. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 504 undefin ed on input line 55682. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 504 undefined on input line 55684. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 504 undefi ned on input line 55684. [504] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 505 undefined on input line 55818. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 505 undefi ned on input line 55818. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 505 und efined on input line 55829. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 505 undefined on input line 55829. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 505 und efined on input line 55831. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 505 undefined on input line 55831. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 505 undefined on input line 55836. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 505 undefi ned on input line 55836. [505] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 506 undefined on input line 55857. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 506 undefi ned on input line 55857. LaTeX Warning: Hyper reference `reference-manual/references:refcp2k2020' on pag e 506 undefined on input line 55888. LaTeX Warning: Reference `reference-manual/references:refcp2k2020' on page 506 undefined on input line 55888. LaTeX Warning: Hyper reference `reference-manual/references:reflaino2005' on pa ge 506 undefined on input line 55895. LaTeX Warning: Reference `reference-manual/references:reflaino2005' on page 506 undefined on input line 55895. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 506 u ndefined on input line 55931. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 506 undefin ed on input line 55931. [506] LaTeX Warning: Hyper reference `install-guide/index:installing-with-cp2k' on pa ge 507 undefined on input line 55938. LaTeX Warning: Reference `install-guide/index:installing-with-cp2k' on page 507 undefined on input line 55938. LaTeX Warning: Hyper reference `reference-manual/special/free-energy-implementa tion:dgimplement' on page 507 undefined on input line 55947. LaTeX Warning: Reference `reference-manual/special/free-energy-implementation:d gimplement' on page 507 undefined on input line 55947. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 507 undefined on input line 55959. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 507 undefi ned on input line 55959. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 507 u ndefined on input line 55960. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 507 undefin ed on input line 55960. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmgroup' o n page 507 undefined on input line 55973. LaTeX Warning: Reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmgroup' on page 507 undefined on input line 55973. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 507 undefined on input line 55973. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 507 undefi ned on input line 55973. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmcharge' on page 507 undefined on input line 55983. LaTeX Warning: Reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmcharge' on pag e 507 undefined on input line 55983. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmmultipli city' on page 507 undefined on input line 55983. LaTeX Warning: Reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmmultiplicity' on page 507 undefined on input line 55983. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmmethod' on page 507 undefined on input line 55990. LaTeX Warning: Reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmmethod' on pag e 507 undefined on input line 55990. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 507 undefined on input line 55990. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 507 undefi ned on input line 55990. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmme thod-PBE' on page 507 undefined on input line 55996. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmmethod-P BE' on page 507 undefined on input line 55996. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmme thod-BLYP' on page 507 undefined on input line 56000. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmmethod-B LYP' on page 507 undefined on input line 56000. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmme thod-INPUT' on page 507 undefined on input line 56013. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-qmmm-cp2k-qmmethod-I NPUT' on page 507 undefined on input line 56013. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 507 u ndefined on input line 56014. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 507 undefin ed on input line 56014. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 507 undefined on input line 56015. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 507 undefi ned on input line 56015. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 507 undefined on input line 56032. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 507 undefi ned on input line 56032. [507] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 508 und efined on input line 56048. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 508 undefined on input line 56048. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 508 undefined on input line 56049. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 508 undefi ned on input line 56049. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 508 undefined on input line 56050. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 508 undefi ned on input line 56050. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmfilename s' on page 508 undefined on input line 56052. LaTeX Warning: Reference `user-guide/mdp-options:mdp-qmmm-cp2k-qmfilenames' on page 508 undefined on input line 56052. LaTeX Warning: Hyper reference `reference-manual/special/qmmm:qmmm' on page 508 undefined on input line 56082. LaTeX Warning: Reference `reference-manual/special/qmmm:qmmm' on page 508 undef ined on input line 56082. LaTeX Warning: Hyper reference `reference-manual/references:refroethlisbergerqm mm' on page 508 undefined on input line 56096. LaTeX Warning: Reference `reference-manual/references:refroethlisbergerqmmm' on page 508 undefined on input line 56096. [508] LaTeX Warning: Hyper reference `reference-manual/references:refroethlisbergerqm mm' on page 509 undefined on input line 56165. LaTeX Warning: Reference `reference-manual/references:refroethlisbergerqmmm' on page 509 undefined on input line 56165. LaTeX Warning: Hyper reference `reference-manual/references:refroethlisbergerqm mm' on page 509 undefined on input line 56178. LaTeX Warning: Reference `reference-manual/references:refroethlisbergerqmmm' on page 509 undefined on input line 56178. LaTeX Warning: Hyper reference `install-guide/index:installing-with-mimic' on p age 509 undefined on input line 56212. LaTeX Warning: Reference `install-guide/index:installing-with-mimic' on page 50 9 undefined on input line 56212. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 509 undefined on input line 56247. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 509 undefi ned on input line 56247. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-integrator-mim ic' on page 509 undefined on input line 56253. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-integrator-mimic' on page 509 undefined on input line 56253. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 509 undefined on input line 56263. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 509 undefi ned on input line 56263. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 509 undefined on input line 56267. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 509 undefi ned on input line 56267. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 509 u ndefined on input line 56267. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 509 undefin ed on input line 56267. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 509 u ndefined on input line 56267. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 509 undefin ed on input line 56267. [509] [510] [511] LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 512 undefined on input line 56472. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 512 undefi ned on input line 56472. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56474. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56474. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 512 u ndefined on input line 56476. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 512 undefin ed on input line 56476. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 512 undefined on input line 56477. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 512 undefi ned on input line 56477. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 512 u ndefined on input line 56478. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 512 undefin ed on input line 56478. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56485. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56485. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56487. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56487. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56492. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56492. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56497. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56497. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56510. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56510. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 und efined on input line 56512. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 512 undefined on input line 56512. [512] LaTeX Warning: Hyper reference `reference-manual/references:refyesylevskyy2007' on page 513 undefined on input line 56542. LaTeX Warning: Reference `reference-manual/references:refyesylevskyy2007' on pa ge 513 undefined on input line 56542. LaTeX Warning: Hyper reference `reference-manual/references:refwolf2010' on pag e 513 undefined on input line 56543. LaTeX Warning: Reference `reference-manual/references:refwolf2010' on page 513 undefined on input line 56543. [513] LaTeX Warning: Hyper reference `reference-manual/references:reforzechowski2008' on page 514 undefined on input line 56569. LaTeX Warning: Reference `reference-manual/references:reforzechowski2008' on pa ge 514 undefined on input line 56569. LaTeX Warning: Hyper reference `reference-manual/references:refigaev2019' on pa ge 514 undefined on input line 56569. LaTeX Warning: Reference `reference-manual/references:refigaev2019' on page 514 undefined on input line 56569. [514] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-density-guided-simul ation-nst' on page 515 undefined on input line 56746. LaTeX Warning: Reference `user-guide/mdp-options:mdp-density-guided-simulation- nst' on page 515 undefined on input line 56746. [515] [516] LaTeX Warning: Hyper reference `reference-manual/references:reffiorin13' on pag e 517 undefined on input line 56862. LaTeX Warning: Reference `reference-manual/references:reffiorin13' on page 517 undefined on input line 56862. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 517 undefined on input line 56870. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 517 undefi ned on input line 56870. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-colvars' on page 517 undefined on input line 56878. LaTeX Warning: Reference `user-guide/mdp-options:mdp-colvars' on page 517 undef ined on input line 56878. LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 517 undefined on input line 56899. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 517 undefi ned on input line 56899. [517] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 518 u ndefined on input line 56996. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 518 undefin ed on input line 56996. LaTeX Warning: Hyper reference `install-guide/index:installing-with-neural-netw ork-potential-support' on page 518 undefined on input line 57005. LaTeX Warning: Reference `install-guide/index:installing-with-neural-network-po tential-support' on page 518 undefined on input line 57005. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 518 undefined on input line 57011. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 518 undefi ned on input line 57011. [518] [519] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 520 u ndefined on input line 57110. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 520 undefin ed on input line 57110. LaTeX Warning: Hyper reference `onlinehelp/gmx-help:gmx-help' on page 520 undef ined on input line 57112. LaTeX Warning: Reference `onlinehelp/gmx-help:gmx-help' on page 520 undefined o n input line 57112. LaTeX Warning: Hyper reference `reference-manual/file-formats::doc' on page 520 undefined on input line 57119. LaTeX Warning: Reference `reference-manual/file-formats::doc' on page 520 undef ined on input line 57119. LaTeX Warning: Hyper reference `reference-manual/file-formats:mdp' on page 520 undefined on input line 57131. LaTeX Warning: Reference `reference-manual/file-formats:mdp' on page 520 undefi ned on input line 57131. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-general' on page 520 undefined on input line 57133. LaTeX Warning: Reference `user-guide/mdp-options:mdp-general' on page 520 undef ined on input line 57133. [520] LaTeX Warning: Hyper reference `user-guide/cmdline:gmx-cmdline' on page 521 und efined on input line 57146. LaTeX Warning: Reference `user-guide/cmdline:gmx-cmdline' on page 521 undefined on input line 57146. LaTeX Warning: Hyper reference `reference-manual/analysis/using-groups:usinggro ups' on page 521 undefined on input line 57151. LaTeX Warning: Reference `reference-manual/analysis/using-groups:usinggroups' o n page 521 undefined on input line 57151. LaTeX Warning: Hyper reference `reference-manual/analysis/using-groups:selectio ns' on page 521 undefined on input line 57152. LaTeX Warning: Reference `reference-manual/analysis/using-groups:selections' on page 521 undefined on input line 57152. LaTeX Warning: Hyper reference `reference-manual/algorithms/algorithms:algorith ms' on page 521 undefined on input line 57162. LaTeX Warning: Reference `reference-manual/algorithms/algorithms:algorithms' on page 521 undefined on input line 57162. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 521 und efined on input line 57163. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 521 undefined on input line 57163. LaTeX Warning: Hyper reference `reference-manual/algorithms/group-concept:group concept' on page 521 undefined on input line 57163. LaTeX Warning: Reference `reference-manual/algorithms/group-concept:groupconcep t' on page 521 undefined on input line 57163. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 521 undefined on input line 57194. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 521 undefi ned on input line 57194. LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 5 21 undefined on input line 57197. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 521 und efined on input line 57197. LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 521 u ndefined on input line 57198. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 521 undefin ed on input line 57198. LaTeX Warning: Hyper reference `onlinehelp/gmx-mk_angndx:gmx-mk-angndx' on page 521 undefined on input line 57199. LaTeX Warning: Reference `onlinehelp/gmx-mk_angndx:gmx-mk-angndx' on page 521 u ndefined on input line 57199. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 521 u ndefined on input line 57229. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 521 undefin ed on input line 57229. [521] LaTeX Warning: Hyper reference `reference-manual/topologies/particle-type:vsite top' on page 522 undefined on input line 57290. LaTeX Warning: Reference `reference-manual/topologies/particle-type:vsitetop' o n page 522 undefined on input line 57290. [522] LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 523 u ndefined on input line 57359. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 523 undefin ed on input line 57359. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 523 undefined on input line 57394. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 523 undefi ned on input line 57394. LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 523 u ndefined on input line 57400. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 523 undefin ed on input line 57400. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 523 undefined on input line 57404. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 523 undefi ned on input line 57404. LaTeX Warning: Hyper reference `onlinehelp/gmx-help:gmx-help' on page 523 undef ined on input line 57412. LaTeX Warning: Reference `onlinehelp/gmx-help:gmx-help' on page 523 undefined o n input line 57412. LaTeX Warning: Hyper reference `onlinehelp/gmx-help:gmx-help' on page 523 undef ined on input line 57414. LaTeX Warning: Reference `onlinehelp/gmx-help:gmx-help' on page 523 undefined o n input line 57414. LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 523 u ndefined on input line 57425. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 523 undefin ed on input line 57425. [523] LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 524 u ndefined on input line 57457. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 524 undefin ed on input line 57457. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 524 undef ined on input line 57457. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 524 undefined o n input line 57457. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 524 u ndefined on input line 57460. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 524 undefin ed on input line 57460. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 524 undef ined on input line 57472. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 524 undefined o n input line 57472. LaTeX Warning: Hyper reference `reference-manual/algorithms/algorithms:algorith ms' on page 524 undefined on input line 57474. LaTeX Warning: Reference `reference-manual/algorithms/algorithms:algorithms' on page 524 undefined on input line 57474. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefin ed on input line 57482. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefined on input line 57482. LaTeX Warning: Hyper reference `reference-manual/analysis/radial-distribution-f unction:fig-rdfex' on page 524 undefined on input line 57500. LaTeX Warning: Reference `reference-manual/analysis/radial-distribution-functio n:fig-rdfex' on page 524 undefined on input line 57500. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefin ed on input line 57511. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefined on input line 57511. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefin ed on input line 57511. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefined on input line 57511. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefin ed on input line 57516. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefined on input line 57516. LaTeX Warning: Hyper reference `reference-manual/analysis/radial-distribution-f unction:fig-rdfex' on page 524 undefined on input line 57518. LaTeX Warning: Reference `reference-manual/analysis/radial-distribution-functio n:fig-rdfex' on page 524 undefined on input line 57518. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen81' on page 524 undefined on input line 57520. LaTeX Warning: Reference `reference-manual/references:refberendsen81' on page 5 24 undefined on input line 57520. LaTeX Warning: Hyper reference `reference-manual/analysis/radial-distribution-f unction:fig-rdf' on page 524 undefined on input line 57520. LaTeX Warning: Reference `reference-manual/analysis/radial-distribution-functio n:fig-rdf' on page 524 undefined on input line 57520. LaTeX Warning: Hyper reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefin ed on input line 57530. LaTeX Warning: Reference `onlinehelp/gmx-rdf:gmx-rdf' on page 524 undefined on input line 57530. LaTeX Warning: Hyper reference `reference-manual/analysis/radial-distribution-f unction:fig-rdfex' on page 524 undefined on input line 57533. LaTeX Warning: Reference `reference-manual/analysis/radial-distribution-functio n:fig-rdfex' on page 524 undefined on input line 57533. [524 <./rdf.pdf>] LaTeX Warning: Hyper reference `reference-manual/analysis/radial-distribution-f unction:fig-rdfex' on page 525 undefined on input line 57546. LaTeX Warning: Reference `reference-manual/analysis/radial-distribution-functio n:fig-rdfex' on page 525 undefined on input line 57546. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 525 undefined on input line 57557. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 525 u ndefined on input line 57557. LaTeX Warning: Reference `equation:reference-manual/analysis/correlation-functi on:eqncorrmd' on page 525 undefined on input line 57595. [525 <./rdfO-O.pdf>] LaTeX Warning: Reference `equation:reference-manual/analysis/correlation-functi on:eqncorr' on page 526 undefined on input line 57611. LaTeX Warning: Reference `equation:reference-manual/analysis/correlation-functi on:eqncorrmd' on page 526 undefined on input line 57628. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 526 undefined on input line 57630. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 526 u ndefined on input line 57630. LaTeX Warning: Reference `equation:reference-manual/analysis/correlation-functi on:eqncorrleg' on page 526 undefined on input line 57650. LaTeX Warning: Hyper reference `onlinehelp/gmx-rotacf:gmx-rotacf' on page 526 u ndefined on input line 57651. LaTeX Warning: Reference `onlinehelp/gmx-rotacf:gmx-rotacf' on page 526 undefin ed on input line 57651. LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 526 undefined on input line 57652. LaTeX Warning: Reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 526 undef ined on input line 57652. LaTeX Warning: Hyper reference `reference-manual/references:refspoel97a' on pag e 526 undefined on input line 57656. LaTeX Warning: Reference `reference-manual/references:refspoel97a' on page 526 undefined on input line 57656. LaTeX Warning: Hyper reference `onlinehelp/gmx-velacc:gmx-velacc' on page 526 u ndefined on input line 57671. LaTeX Warning: Reference `onlinehelp/gmx-velacc:gmx-velacc' on page 526 undefin ed on input line 57671. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 526 undefined on input line 57678. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 526 u ndefined on input line 57678. LaTeX Warning: Hyper reference `reference-manual/analysis/mean-square-displacem ent:msd' on page 526 undefined on input line 57685. LaTeX Warning: Reference `reference-manual/analysis/mean-square-displacement:ms d' on page 526 undefined on input line 57685. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 526 undefined on input line 57687. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 526 u ndefined on input line 57687. LaTeX Warning: Hyper reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 526 undefined on input line 57694. LaTeX Warning: Reference `onlinehelp/gmx-dipoles:gmx-dipoles' on page 526 undef ined on input line 57694. [526] LaTeX Warning: Reference `equation:reference-manual/analysis/correlation-functi on:eqncorrtime' on page 527 undefined on input line 57701. LaTeX Warning: Hyper reference `reference-manual/references:refpsmith93c' on pa ge 527 undefined on input line 57708. LaTeX Warning: Reference `reference-manual/references:refpsmith93c' on page 527 undefined on input line 57708. LaTeX Warning: Hyper reference `reference-manual/references:refbalasubramanian9 6' on page 527 undefined on input line 57709. LaTeX Warning: Reference `reference-manual/references:refbalasubramanian96' on page 527 undefined on input line 57709. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 527 u ndefined on input line 57709. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 527 undefin ed on input line 57709. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002a' on pa ge 527 undefined on input line 57710. LaTeX Warning: Reference `reference-manual/references:refhess2002a' on page 527 undefined on input line 57710. LaTeX Warning: Hyper reference `reference-manual/analysis/curve-fitting:table-f itfn' on page 527 undefined on input line 57726. LaTeX Warning: Reference `reference-manual/analysis/curve-fitting:table-fitfn' on page 527 undefined on input line 57726. LaTeX Warning: Hyper reference `reference-manual/references:reflmfit' on page 5 27 undefined on input line 57728. LaTeX Warning: Reference `reference-manual/references:reflmfit' on page 527 und efined on input line 57728. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002a' on pa ge 527 undefined on input line 57820. LaTeX Warning: Reference `reference-manual/references:refhess2002a' on page 527 undefined on input line 57820. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze:gmx-analyze' on page 527 undefined on input line 57830. LaTeX Warning: Reference `onlinehelp/gmx-analyze:gmx-analyze' on page 527 undef ined on input line 57830. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002a' on pa ge 527 undefined on input line 57836. LaTeX Warning: Reference `reference-manual/references:refhess2002a' on page 527 undefined on input line 57836. LaTeX Warning: Hyper reference `reference-manual/references:refsteen-saethre201 4a' on page 527 undefined on input line 57852. LaTeX Warning: Reference `reference-manual/references:refsteen-saethre2014a' on page 527 undefined on input line 57852. LaTeX Warning: Hyper reference `onlinehelp/gmx-densorder:gmx-densorder' on page 527 undefined on input line 57853. LaTeX Warning: Reference `onlinehelp/gmx-densorder:gmx-densorder' on page 527 u ndefined on input line 57853. [527] LaTeX Warning: Hyper reference `reference-manual/references:refpalmer1994a' on page 528 undefined on input line 57860. LaTeX Warning: Reference `reference-manual/references:refpalmer1994a' on page 5 28 undefined on input line 57860. LaTeX Warning: Hyper reference `onlinehelp/gmx-tcaf:gmx-tcaf' on page 528 undef ined on input line 57868. LaTeX Warning: Reference `onlinehelp/gmx-tcaf:gmx-tcaf' on page 528 undefined o n input line 57868. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002a' on pa ge 528 undefined on input line 57875. LaTeX Warning: Reference `reference-manual/references:refhess2002a' on page 528 undefined on input line 57875. LaTeX Warning: Hyper reference `reference-manual/references:refwensink2003a' on page 528 undefined on input line 57875. LaTeX Warning: Reference `reference-manual/references:refwensink2003a' on page 528 undefined on input line 57875. LaTeX Warning: Hyper reference `reference-manual/references:refpsmith93c' on pa ge 528 undefined on input line 57877. LaTeX Warning: Reference `reference-manual/references:refpsmith93c' on page 528 undefined on input line 57877. LaTeX Warning: Hyper reference `reference-manual/references:refguo2002b' on pag e 528 undefined on input line 57879. LaTeX Warning: Reference `reference-manual/references:refguo2002b' on page 528 undefined on input line 57879. LaTeX Warning: Hyper reference `reference-manual/references:reffanourgakis2012a ' on page 528 undefined on input line 57898. LaTeX Warning: Reference `reference-manual/references:reffanourgakis2012a' on p age 528 undefined on input line 57898. LaTeX Warning: Hyper reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefin ed on input line 57906. LaTeX Warning: Reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefined on input line 57906. LaTeX Warning: Hyper reference `reference-manual/references:refallen87' on page 528 undefined on input line 57910. LaTeX Warning: Reference `reference-manual/references:refallen87' on page 528 u ndefined on input line 57910. LaTeX Warning: Hyper reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefin ed on input line 57920. LaTeX Warning: Reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefined on input line 57920. LaTeX Warning: Hyper reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefin ed on input line 57926. LaTeX Warning: Reference `onlinehelp/gmx-msd:gmx-msd' on page 528 undefined on input line 57926. LaTeX Warning: Hyper reference `reference-manual/analysis/mean-square-displacem ent:fig-msdwater' on page 528 undefined on input line 57933. LaTeX Warning: Reference `reference-manual/analysis/mean-square-displacement:fi g-msdwater' on page 528 undefined on input line 57933. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 5 28 undefined on input line 57948. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 528 und efined on input line 57948. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 528 und efined on input line 57948. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 528 undefined on input line 57948. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 528 u ndefined on input line 57949. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 528 undefin ed on input line 57949. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 5 28 undefined on input line 57952. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 528 und efined on input line 57952. [528] LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 529 und efined on input line 57989. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 529 undefined on input line 57989. LaTeX Warning: Hyper reference `reference-manual/analysis/bond-angle-dihedral:f ig-dihdef' on page 529 undefined on input line 58009. LaTeX Warning: Reference `reference-manual/analysis/bond-angle-dihedral:fig-dih def' on page 529 undefined on input line 58009. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 529 u ndefined on input line 58020. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 529 undefin ed on input line 58020. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 529 und efined on input line 58023. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 529 undefined on input line 58023. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 529 u ndefined on input line 58029. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 529 undefin ed on input line 58029. LaTeX Warning: Hyper reference `reference-manual/analysis/bond-angle-dihedral:f ig-sgangle' on page 529 undefined on input line 58031. LaTeX Warning: Reference `reference-manual/analysis/bond-angle-dihedral:fig-sga ngle' on page 529 undefined on input line 58031. [529 <./msdwater.pdf>] LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 530 u ndefined on input line 58042. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 530 undefin ed on input line 58042. LaTeX Warning: Hyper reference `onlinehelp/gmx-gangle:gmx-gangle' on page 530 u ndefined on input line 58042. LaTeX Warning: Reference `onlinehelp/gmx-gangle:gmx-gangle' on page 530 undefin ed on input line 58042. LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate:gmx-gyrate' on page 530 u ndefined on input line 58050. LaTeX Warning: Reference `onlinehelp/gmx-gyrate:gmx-gyrate' on page 530 undefin ed on input line 58050. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 5 30 undefined on input line 58050. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 530 und efined on input line 58050. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undefined on input line 58051. LaTeX Warning: Reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undef ined on input line 58051. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdmat:gmx-mdmat' on page 530 und efined on input line 58051. LaTeX Warning: Reference `onlinehelp/gmx-mdmat:gmx-mdmat' on page 530 undefined on input line 58051. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 5 30 undefined on input line 58052. LaTeX Warning: Reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 530 und efined on input line 58052. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 530 u ndefined on input line 58052. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 530 undefin ed on input line 58052. LaTeX Warning: Hyper reference `onlinehelp/gmx-gyrate:gmx-gyrate' on page 530 u ndefined on input line 58055. LaTeX Warning: Reference `onlinehelp/gmx-gyrate:gmx-gyrate' on page 530 undefin ed on input line 58055. LaTeX Warning: Hyper reference `onlinehelp/gmx-distance:gmx-distance' on page 5 30 undefined on input line 58085. LaTeX Warning: Reference `onlinehelp/gmx-distance:gmx-distance' on page 530 und efined on input line 58085. LaTeX Warning: Hyper reference `reference-manual/analysis/bond-angle-dihedral:b ad' on page 530 undefined on input line 58086. LaTeX Warning: Reference `reference-manual/analysis/bond-angle-dihedral:bad' on page 530 undefined on input line 58086. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undefined on input line 58091. LaTeX Warning: Reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undef ined on input line 58091. LaTeX Warning: Hyper reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 5 30 undefined on input line 58097. LaTeX Warning: Reference `onlinehelp/gmx-pairdist:gmx-pairdist' on page 530 und efined on input line 58097. LaTeX Warning: Hyper reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undefined on input line 58097. LaTeX Warning: Reference `onlinehelp/gmx-mindist:gmx-mindist' on page 530 undef ined on input line 58097. [530 <./dih-def.pdf> <./sgangle.pdf pdfTeX warning: /usr/bin/pdflatex (file ./sgangle.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdmat:gmx-mdmat' on page 531 und efined on input line 58102. LaTeX Warning: Reference `onlinehelp/gmx-mdmat:gmx-mdmat' on page 531 undefined on input line 58102. LaTeX Warning: Hyper reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 531 u ndefined on input line 58109. LaTeX Warning: Reference `onlinehelp/gmx-xpm2ps:gmx-xpm2ps' on page 531 undefin ed on input line 58109. LaTeX Warning: Hyper reference `reference-manual/analysis/radius-of-gyration:fi g-distm' on page 531 undefined on input line 58110. LaTeX Warning: Reference `reference-manual/analysis/radius-of-gyration:fig-dist m' on page 531 undefined on input line 58110. LaTeX Warning: Hyper reference `reference-manual/references:refspoel96b' on pag e 531 undefined on input line 58120. LaTeX Warning: Reference `reference-manual/references:refspoel96b' on page 531 undefined on input line 58120. LaTeX Warning: Hyper reference `onlinehelp/gmx-rms:gmx-rms' on page 531 undefin ed on input line 58135. LaTeX Warning: Reference `onlinehelp/gmx-rms:gmx-rms' on page 531 undefined on input line 58135. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsdist:gmx-rmsdist' on page 531 undefined on input line 58135. LaTeX Warning: Reference `onlinehelp/gmx-rmsdist:gmx-rmsdist' on page 531 undef ined on input line 58135. LaTeX Warning: Hyper reference `onlinehelp/gmx-rms:gmx-rms' on page 531 undefin ed on input line 58138. LaTeX Warning: Reference `onlinehelp/gmx-rms:gmx-rms' on page 531 undefined on input line 58138. LaTeX Warning: Reference `equation:reference-manual/analysis/rmsd:eqnrmsd' on p age 531 undefined on input line 58140. LaTeX Warning: Reference `equation:reference-manual/analysis/rmsd:eqnrmsd' on p age 531 undefined on input line 58159. LaTeX Warning: Hyper reference `onlinehelp/gmx-rmsdist:gmx-rmsdist' on page 531 undefined on input line 58168. LaTeX Warning: Reference `onlinehelp/gmx-rmsdist:gmx-rmsdist' on page 531 undef ined on input line 58168. [531 <./distm.pdf>] LaTeX Warning: Hyper reference `reference-manual/references:refamadei93' on pag e 532 undefined on input line 58184. LaTeX Warning: Reference `reference-manual/references:refamadei93' on page 532 undefined on input line 58184. LaTeX Warning: Hyper reference `reference-manual/references:refhess2002b' on pa ge 532 undefined on input line 58238. LaTeX Warning: Reference `reference-manual/references:refhess2002b' on page 532 undefined on input line 58238. [532] LaTeX Warning: Hyper reference `reference-manual/references:refhess2002b' on pa ge 533 undefined on input line 58297. LaTeX Warning: Reference `reference-manual/references:refhess2002b' on page 533 undefined on input line 58297. LaTeX Warning: Hyper reference `reference-manual/references:refhess2000' on pag e 533 undefined on input line 58297. LaTeX Warning: Reference `reference-manual/references:refhess2000' on page 533 undefined on input line 58297. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar:gmx-covar' on page 533 und efined on input line 58312. LaTeX Warning: Reference `onlinehelp/gmx-covar:gmx-covar' on page 533 undefined on input line 58312. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 u ndefined on input line 58314. LaTeX Warning: Reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 undefin ed on input line 58314. LaTeX Warning: Hyper reference `onlinehelp/gmx-analyze:gmx-analyze' on page 533 undefined on input line 58316. LaTeX Warning: Reference `onlinehelp/gmx-analyze:gmx-analyze' on page 533 undef ined on input line 58316. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 533 und efined on input line 58324. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 533 undefined on input line 58324. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar:gmx-covar' on page 533 und efined on input line 58324. LaTeX Warning: Reference `onlinehelp/gmx-covar:gmx-covar' on page 533 undefined on input line 58324. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 u ndefined on input line 58325. LaTeX Warning: Reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 undefin ed on input line 58325. LaTeX Warning: Hyper reference `reference-manual/references:refmu2005a' on page 533 undefined on input line 58327. LaTeX Warning: Reference `reference-manual/references:refmu2005a' on page 533 u ndefined on input line 58327. LaTeX Warning: Hyper reference `onlinehelp/gmx-mk_angndx:gmx-mk-angndx' on page 533 undefined on input line 58329. LaTeX Warning: Reference `onlinehelp/gmx-mk_angndx:gmx-mk-angndx' on page 533 u ndefined on input line 58329. LaTeX Warning: Hyper reference `onlinehelp/gmx-angle:gmx-angle' on page 533 und efined on input line 58330. LaTeX Warning: Reference `onlinehelp/gmx-angle:gmx-angle' on page 533 undefined on input line 58330. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 533 undefined on input line 58331. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 533 undefi ned on input line 58331. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 533 undefined on input line 58333. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 533 undefi ned on input line 58333. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 533 undefined on input line 58337. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 533 undefi ned on input line 58337. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar:gmx-covar' on page 533 und efined on input line 58338. LaTeX Warning: Reference `onlinehelp/gmx-covar:gmx-covar' on page 533 undefined on input line 58338. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 533 undefined on input line 58340. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 533 undefi ned on input line 58340. LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 533 undefined on input line 58341. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 533 undefi ned on input line 58341. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 533 undefined on input line 58341. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 533 undefi ned on input line 58341. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 533 undefined on input line 58342. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 533 undefi ned on input line 58342. LaTeX Warning: Hyper reference `onlinehelp/gmx-covar:gmx-covar' on page 533 und efined on input line 58345. LaTeX Warning: Reference `onlinehelp/gmx-covar:gmx-covar' on page 533 undefined on input line 58345. LaTeX Warning: Hyper reference `reference-manual/file-formats:trr' on page 533 undefined on input line 58347. LaTeX Warning: Reference `reference-manual/file-formats:trr' on page 533 undefi ned on input line 58347. LaTeX Warning: Hyper reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 u ndefined on input line 58348. LaTeX Warning: Reference `onlinehelp/gmx-anaeig:gmx-anaeig' on page 533 undefin ed on input line 58348. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 und efined on input line 58357. LaTeX Warning: Reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 undefined on input line 58357. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 und efined on input line 58358. LaTeX Warning: Reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 undefined on input line 58358. LaTeX Warning: Hyper reference `reference-manual/analysis/hydrogen-bonds:fig-hb ond' on page 533 undefined on input line 58361. LaTeX Warning: Reference `reference-manual/analysis/hydrogen-bonds:fig-hbond' o n page 533 undefined on input line 58361. LaTeX Warning: Hyper reference `reference-manual/analysis/hydrogen-bonds:fig-hb ondinsert' on page 533 undefined on input line 58380. LaTeX Warning: Reference `reference-manual/analysis/hydrogen-bonds:fig-hbondins ert' on page 533 undefined on input line 58380. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 und efined on input line 58383. LaTeX Warning: Reference `onlinehelp/gmx-hbond:gmx-hbond' on page 533 undefined on input line 58383. [533] LaTeX Warning: Hyper reference `reference-manual/references:refspoel2006b' on p age 534 undefined on input line 58443. LaTeX Warning: Reference `reference-manual/references:refspoel2006b' on page 53 4 undefined on input line 58443. LaTeX Warning: Hyper reference `reference-manual/references:refluzar96b' on pag e 534 undefined on input line 58444. LaTeX Warning: Reference `reference-manual/references:refluzar96b' on page 534 undefined on input line 58444. LaTeX Warning: Hyper reference `reference-manual/references:refluzar2000a' on p age 534 undefined on input line 58444. LaTeX Warning: Reference `reference-manual/references:refluzar2000a' on page 53 4 undefined on input line 58444. [534 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `onlinehelp/gmx-dssp:gmx-dssp' on page 535 undef ined on input line 58469. LaTeX Warning: Reference `onlinehelp/gmx-dssp:gmx-dssp' on page 535 undefined o n input line 58469. LaTeX Warning: Hyper reference `onlinehelp/gmx-rama:gmx-rama' on page 535 undef ined on input line 58469. LaTeX Warning: Reference `onlinehelp/gmx-rama:gmx-rama' on page 535 undefined o n input line 58469. LaTeX Warning: Hyper reference `onlinehelp/gmx-wheel:gmx-wheel' on page 535 und efined on input line 58470. LaTeX Warning: Reference `onlinehelp/gmx-wheel:gmx-wheel' on page 535 undefined on input line 58470. LaTeX Warning: Hyper reference `reference-manual/analysis/radius-of-gyration:rg ' on page 535 undefined on input line 58473. LaTeX Warning: Reference `reference-manual/analysis/radius-of-gyration:rg' on p age 535 undefined on input line 58473. LaTeX Warning: Hyper reference `reference-manual/analysis/rmsd:rmsd' on page 53 5 undefined on input line 58473. LaTeX Warning: Reference `reference-manual/analysis/rmsd:rmsd' on page 535 unde fined on input line 58473. LaTeX Warning: Hyper reference `onlinehelp/gmx-dssp:gmx-dssp' on page 535 undef ined on input line 58479. LaTeX Warning: Reference `onlinehelp/gmx-dssp:gmx-dssp' on page 535 undefined o n input line 58479. LaTeX Warning: Hyper reference `reference-manual/references:refkabsch83' on pag e 535 undefined on input line 58480. LaTeX Warning: Reference `reference-manual/references:refkabsch83' on page 535 undefined on input line 58480. LaTeX Warning: Hyper reference `reference-manual/analysis/protein-related:fig-p hipsi' on page 535 undefined on input line 58495. LaTeX Warning: Reference `reference-manual/analysis/protein-related:fig-phipsi' on page 535 undefined on input line 58495. LaTeX Warning: Hyper reference `onlinehelp/gmx-rama:gmx-rama' on page 535 undef ined on input line 58507. LaTeX Warning: Reference `onlinehelp/gmx-rama:gmx-rama' on page 535 undefined o n input line 58507. LaTeX Warning: Hyper reference `reference-manual/analysis/protein-related:fig-r ama' on page 535 undefined on input line 58508. LaTeX Warning: Reference `reference-manual/analysis/protein-related:fig-rama' o n page 535 undefined on input line 58508. LaTeX Warning: Hyper reference `onlinehelp/gmx-wheel:gmx-wheel' on page 535 und efined on input line 58520. LaTeX Warning: Reference `onlinehelp/gmx-wheel:gmx-wheel' on page 535 undefined on input line 58520. LaTeX Warning: Hyper reference `reference-manual/analysis/protein-related:fig-h prwheel' on page 535 undefined on input line 58522. LaTeX Warning: Reference `reference-manual/analysis/protein-related:fig-hprwhee l' on page 535 undefined on input line 58522. LaTeX Warning: Hyper reference `onlinehelp/gmx-order:gmx-order' on page 535 und efined on input line 58537. LaTeX Warning: Reference `onlinehelp/gmx-order:gmx-order' on page 535 undefined on input line 58537. LaTeX Warning: Hyper reference `onlinehelp/gmx-density:gmx-density' on page 535 undefined on input line 58537. LaTeX Warning: Reference `onlinehelp/gmx-density:gmx-density' on page 535 undef ined on input line 58537. LaTeX Warning: Hyper reference `onlinehelp/gmx-potential:gmx-potential' on page 535 undefined on input line 58538. LaTeX Warning: Reference `onlinehelp/gmx-potential:gmx-potential' on page 535 u ndefined on input line 58538. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 535 undef ined on input line 58538. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 535 undefined o n input line 58538. LaTeX Warning: Hyper reference `onlinehelp/gmx-order:gmx-order' on page 535 und efined on input line 58542. LaTeX Warning: Reference `onlinehelp/gmx-order:gmx-order' on page 535 undefined on input line 58542. [535 <./phipsi.pdf>] [536 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `onlinehelp/gmx-potential:gmx-potential' on page 537 undefined on input line 58577. LaTeX Warning: Reference `onlinehelp/gmx-potential:gmx-potential' on page 537 u ndefined on input line 58577. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 537 undef ined on input line 58584. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 537 undefined o n input line 58584. LaTeX Warning: Hyper reference `onlinehelp/gmx-density:gmx-density' on page 537 undefined on input line 58593. LaTeX Warning: Reference `onlinehelp/gmx-density:gmx-density' on page 537 undef ined on input line 58593. [537] LaTeX Warning: Hyper reference `reference-manual/references:refbekker93b' on pa ge 538 undefined on input line 58635. LaTeX Warning: Reference `reference-manual/references:refbekker93b' on page 538 undefined on input line 58635. [538] [539 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58763 ...ecular shift (mol\sphinxhyphen{}shift)} ] [540] LaTeX Warning: Hyper reference `reference-manual/references:refberendsen81' on page 541 undefined on input line 58894. LaTeX Warning: Reference `reference-manual/references:refberendsen81' on page 5 41 undefined on input line 58894. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:lj' on page 541 undefined on input line 58907. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:lj' on page 541 undefined on input line 58907. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:coul' on page 541 undefined on input line 58908. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:cou l' on page 541 undefined on input line 58908. LaTeX Warning: Hyper reference `reference-manual/references:refberendsen87' on page 541 undefined on input line 58918. LaTeX Warning: Reference `reference-manual/references:refberendsen87' on page 5 41 undefined on input line 58918. LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen83' on page 541 undefined on input line 58919. LaTeX Warning: Reference `reference-manual/references:refjorgensen83' on page 5 41 undefined on input line 58919. LaTeX Warning: Hyper reference `reference-manual/references:refjorgensen83' on page 541 undefined on input line 58920. LaTeX Warning: Reference `reference-manual/references:refjorgensen83' on page 5 41 undefined on input line 58920. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:lj' on page 541 undefined on input line 58933. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:lj' on page 541 undefined on input line 58933. LaTeX Warning: Hyper reference `reference-manual/functions/nonbonded-interactio ns:coul' on page 541 undefined on input line 58937. LaTeX Warning: Reference `reference-manual/functions/nonbonded-interactions:cou l' on page 541 undefined on input line 58937. [541] LaTeX Warning: Hyper reference `reference-manual/references:refgunsteren94a' on page 542 undefined on input line 58966. LaTeX Warning: Reference `reference-manual/references:refgunsteren94a' on page 542 undefined on input line 58966. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvar1' on page 5 42 undefined on input line 58995. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvar2' on page 5 42 undefined on input line 58996. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvar0' on page 5 42 undefined on input line 58999. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvar1' on page 5 42 undefined on input line 59001. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvarpartial' on page 542 undefined on input line 59033. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsimplevar0' on page 542 undefined on input line 59048. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsimplevar1' on page 542 undefined on input line 59049. [542 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 1}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59057 \end{equation} ] LaTeX Warning: Hyper reference `reference-manual/file-formats:edr' on page 543 undefined on input line 59066. LaTeX Warning: Reference `reference-manual/file-formats:edr' on page 543 undefi ned on input line 59066. LaTeX Warning: Hyper reference `reference-manual/file-formats:log' on page 543 undefined on input line 59079. LaTeX Warning: Reference `reference-manual/file-formats:log' on page 543 undefi ned on input line 59079. LaTeX Warning: Reference `equation:reference-manual/averages:eqnXpartial' on pa ge 543 undefined on input line 59086. LaTeX Warning: Reference `equation:reference-manual/averages:eqnvarpartial' on page 543 undefined on input line 59087. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsimplevar0' on page 543 undefined on input line 59105. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsimplevar1' on page 543 undefined on input line 59106. [543] LaTeX Warning: Reference `equation:reference-manual/averages:eqnpscomb' on page 544 undefined on input line 59167. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsimplevar0' on page 544 undefined on input line 59173. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 544 u ndefined on input line 59179. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 544 undefin ed on input line 59179. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsigma' on page 544 undefined on input line 59194. [544 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... LaTeX Warning: Reference `equation:reference-manual/averages:eqnsumterms' on pa ge 545 undefined on input line 59220. LaTeX Warning: Reference `equation:reference-manual/averages:eqnsigmaterms' on page 545 undefined on input line 59243. [545 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59250 \clearpage ] [546] [547] [548] [549] [550] [551] [552] [553] [554] Chapter 6. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 555 undefined on input line 61005. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 555 undefined on input line 61005. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 555 undefined on input line 61021. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 555 undefined on input line 61021. LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 555 undefined on input line 61031. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 555 undefined on input line 61031. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 555 undefined on input line 61032. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 555 undefined on input line 61032. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 555 undefined on input line 61036. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 555 undefined on input line 61036. [555] LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-venv' on page 5 56 undefined on input line 61097. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-venv' on page 556 und efined on input line 61097. LaTeX Warning: Hyper reference `gmxapi/userguide/install:mpi-requirements' on p age 556 undefined on input line 61106. LaTeX Warning: Reference `gmxapi/userguide/install:mpi-requirements' on page 55 6 undefined on input line 61106. LaTeX Warning: Hyper reference `gmxapi/userguide/install:installation' on page 556 undefined on input line 61134. LaTeX Warning: Reference `gmxapi/userguide/install:installation' on page 556 un defined on input line 61134. [556] LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 557 undefined on input line 61179. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 557 undefined on input line 61179. [557] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 558 undefined on input line 61273. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 558 undefined on input line 61273. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-package-documen tation' on page 558 undefined on input line 61284. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-package-documentation ' on page 558 undefined on input line 61284. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-venv' on page 5 58 undefined on input line 61335. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-venv' on page 558 und efined on input line 61335. [558] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-offline-install ' on page 559 undefined on input line 61393. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-offline-install' on p age 559 undefined on input line 61393. LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 559 undefined on input line 61417. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 559 undefined on input line 61417. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-cmake-hints' on page 559 undefined on input line 61441. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-cmake-hints' on page 559 undefined on input line 61441. [559] [560] LaTeX Warning: Hyper reference `gmxapi/userguide/install:system-site-packages' on page 561 undefined on input line 61542. LaTeX Warning: Reference `gmxapi/userguide/install:system-site-packages' on pag e 561 undefined on input line 61542. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. LaTeX Warning: Hyper reference `gmxapi/userguide/install:mpi-requirements' on p age 561 undefined on input line 61556. LaTeX Warning: Reference `gmxapi/userguide/install:mpi-requirements' on page 56 1 undefined on input line 61556. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 561 undefined on input line 61626. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 561 undefined on input line 61626. [561] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 562 undefined on input line 61715. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 562 undefined on input line 61715. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 562 undefined on input line 61718. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 562 undefined on input line 61718. [562] Underfull \hbox (badness 10000) in paragraph at lines 61748--61751 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi. version' on page 563 undefined on input line 61814. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.versio n' on page 563 undefined on input line 61814. [563] LaTeX Warning: Hyper reference `gmxapi/userguide/install:testing-requirements' on page 564 undefined on input line 61897. LaTeX Warning: Reference `gmxapi/userguide/install:testing-requirements' on pag e 564 undefined on input line 61897. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 564 undefined on input line 61900. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 564 undefined on input line 61900. [564] LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-cmake-hints' on page 565 undefined on input line 61936. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-cmake-hints' on page 565 undefined on input line 61936. LaTeX Warning: Hyper reference `install-guide/index:getting-access-to-gromacs' on page 565 undefined on input line 61991. LaTeX Warning: Reference `install-guide/index:getting-access-to-gromacs' on pag e 565 undefined on input line 61991. [565] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 566 undefined on input line 62069. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 566 undefined on input line 62069. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 566 undefined on input line 62081. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 566 undefined on input line 62081. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 566 undefined on input line 62083. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 566 undefined on input line 62083. [566] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 567 undefined on input line 62106. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 567 undefined on input line 62106. LaTeX Warning: Hyper reference `gmxapi/userguide/install::doc' on page 567 unde fined on input line 62125. LaTeX Warning: Reference `gmxapi/userguide/install::doc' on page 567 undefined on input line 62125. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference::doc' on page 567 undefined on input line 62136. LaTeX Warning: Reference `gmxapi/userguide/pythonreference::doc' on page 567 un defined on input line 62136. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.excepti ons.Error' on page 567 undefined on input line 62140. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.exceptions.Er ror' on page 567 undefined on input line 62140. LaTeX Warning: Hyper reference `gmxapi/userguide/usage:gmxapi-logging' on page 567 undefined on input line 62141. LaTeX Warning: Reference `gmxapi/userguide/usage:gmxapi-logging' on page 567 un defined on input line 62141. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-venv' on page 5 67 undefined on input line 62153. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-venv' on page 567 und efined on input line 62153. LaTeX Warning: Hyper reference `gmxapi/userguide/install:mpi-requirements' on p age 567 undefined on input line 62165. LaTeX Warning: Reference `gmxapi/userguide/install:mpi-requirements' on page 56 7 undefined on input line 62165. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.version .has_feature' on page 567 undefined on input line 62179. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.version.has_f eature' on page 567 undefined on input line 62179. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. [567] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi. simulation' on page 568 undefined on input line 62242. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.simula tion' on page 568 undefined on input line 62242. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.functio n_wrapper' on page 568 undefined on input line 62244. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.function_wrap per' on page 568 undefined on input line 62244. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 568 undefined on input line 62249. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 568 undefined on input line 62249. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 568 undefined on input line 62258. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 568 undefined on input line 62258. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_mpi_environ' on page 568 undefined on input line 62260. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_mpi_environ' on page 568 undefined on input line 62260. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 568 undefined on input line 62264. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 568 undefined on input line 62264. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_mpi_environ' on page 568 undefined on input line 62271. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_mpi_environ' on page 568 undefined on input line 62271. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.functio n_wrapper' on page 568 undefined on input line 62275. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.function_wrap per' on page 568 undefined on input line 62275. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 568 undefined on input line 62276. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 568 undefined on input line 62276. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.read_tp r' on page 568 undefined on input line 62285. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.read_tpr' on page 568 undefined on input line 62285. [568] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure.result' on page 569 undefined on input line 62303. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future.re sult' on page 569 undefined on input line 62303. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 569 undefined on input line 62306. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 569 undefined on input line 62306. LaTeX Warning: Hyper reference `gmxapi/userguide/usage:parallelism' on page 569 undefined on input line 62331. LaTeX Warning: Reference `gmxapi/userguide/usage:parallelism' on page 569 undef ined on input line 62331. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 569 undefined on input line 62365. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 569 undefined on input line 62365. LaTeX Warning: Hyper reference `gmxapi/userguide/usage:parallelism' on page 569 undefined on input line 62373. LaTeX Warning: Reference `gmxapi/userguide/usage:parallelism' on page 569 undef ined on input line 62373. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 569 undefined on input line 62380. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 569 undefined on input line 62380. [569] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.read_tp r' on page 570 undefined on input line 62436. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.read_tpr' on page 570 undefined on input line 62436. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.modify_ input' on page 570 undefined on input line 62439. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.modify_input' on page 570 undefined on input line 62439. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 570 undefined on input line 62440. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 570 undefined on input line 62440. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.functio n_wrapper' on page 570 undefined on input line 62470. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.function_wrap per' on page 570 undefined on input line 62470. [570] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.subgrap h' on page 571 undefined on input line 62533. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.subgraph' on page 571 undefined on input line 62533. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.subgrap h' on page 571 undefined on input line 62550. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.subgraph' on page 571 undefined on input line 62550. [571] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.while_l oop' on page 572 undefined on input line 62564. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.while_loop' o n page 572 undefined on input line 62564. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.while_l oop' on page 572 undefined on input line 62570. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.while_loop' o n page 572 undefined on input line 62570. Overfull \vbox (1.4634pt too high) detected at line 62640 [572] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference::doc' on page 573 undefined on input line 62649. LaTeX Warning: Reference `gmxapi/userguide/pythonreference::doc' on page 573 un defined on input line 62649. LaTeX Warning: Hyper reference `gmxapi/userguide/install:gmxapi-package-documen tation' on page 573 undefined on input line 62686. LaTeX Warning: Reference `gmxapi/userguide/install:gmxapi-package-documentation ' on page 573 undefined on input line 62686. [573] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62768. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62768. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Ope rationReference' on page 574 undefined on input line 62824. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Operation Reference' on page 574 undefined on input line 62824. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62827. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62827. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure.result' on page 574 undefined on input line 62832. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future.re sult' on page 574 undefined on input line 62832. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Ope rationReference.run' on page 574 undefined on input line 62837. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Operation Reference.run' on page 574 undefined on input line 62837. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62842. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62842. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 574 undefined on input line 62844. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 574 undefined on input line 62844. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62847. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62847. LaTeX Warning: Hyper reference `gmxapi/userguide/usage:gmxapi-simulation-prepar ation' on page 574 undefined on input line 62848. LaTeX Warning: Reference `gmxapi/userguide/usage:gmxapi-simulation-preparation' on page 574 undefined on input line 62848. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62858. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62858. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure.result' on page 574 undefined on input line 62859. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future.re sult' on page 574 undefined on input line 62859. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.abc.Fut ure' on page 574 undefined on input line 62863. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.abc.Future' o n page 574 undefined on input line 62863. LaTeX Warning: Hyper reference `gmxapi/userguide/usage:gmxapi-ensemble' on page 574 undefined on input line 62866. LaTeX Warning: Reference `gmxapi/userguide/usage:gmxapi-ensemble' on page 574 u ndefined on input line 62866. [574] [575] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_mpi_environ' on page 576 undefined on input line 63021. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_mpi_environ' on page 576 undefined on input line 63021. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_mpi_environ' on page 576 undefined on input line 63039. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_mpi_environ' on page 576 undefined on input line 63039. [576] [577] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.simulat ion.read_tpr.OutputDataProxy' on page 578 undefined on input line 63284. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.simulation.re ad_tpr.OutputDataProxy' on page 578 undefined on input line 63284. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.read_tp r' on page 578 undefined on input line 63300. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.read_tpr' on page 578 undefined on input line 63300. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.simulat ion.modify_input.OutputDataProxy' on page 578 undefined on input line 63339. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.simulation.mo dify_input.OutputDataProxy' on page 578 undefined on input line 63339. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.modify_ input' on page 578 undefined on input line 63355. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.modify_input' on page 578 undefined on input line 63355. [578] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.simulat ion.mdrun.OutputDataProxy' on page 579 undefined on input line 63410. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.simulation.md run.OutputDataProxy' on page 579 undefined on input line 63410. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 579 undefine d on input line 63439. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 579 undefined on i nput line 63439. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 579 undefined on input line 63458. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 579 undefined on input line 63458. [579] [580] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_prefixes' on page 581 undefined on input line 63814. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_prefixes' on page 581 undefined on input line 63814. [581] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 582 undefined on input line 63895. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 582 undefined on input line 63895. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 582 undefined on input line 63896. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 582 undefined on input line 63896. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi. exceptions' on page 582 undefined on input line 63912. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.except ions' on page 582 undefined on input line 63912. [582] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi. version' on page 583 undefined on input line 64095. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.versio n' on page 583 undefined on input line 64095. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.version .api_is_at_least' on page 583 undefined on input line 64095. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.version.api_i s_at_least' on page 583 undefined on input line 64095. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.version .has_feature' on page 583 undefined on input line 64095. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.version.has_f eature' on page 583 undefined on input line 64095. [583] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.version .api_is_at_least' on page 584 undefined on input line 64182. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.version.api_i s_at_least' on page 584 undefined on input line 64182. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.excepti ons.Error' on page 584 undefined on input line 64197. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.exceptions.Er ror' on page 584 undefined on input line 64197. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.excepti ons.FeatureNotAvailableError' on page 584 undefined on input line 64206. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.exceptions.Fe atureNotAvailableError' on page 584 undefined on input line 64206. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.excepti ons.Error' on page 584 undefined on input line 64242. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.exceptions.Er ror' on page 584 undefined on input line 64242. [584] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .Exception' on page 585 undefined on input line 64315. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Excep tion' on page 585 undefined on input line 64315. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 585 undefined on input line 64340. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 585 undefined on input line 64340. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDSystem' on page 585 undefined on input line 64353. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSys tem' on page 585 undefined on input line 64353. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 585 undefined on input line 64407. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 585 undefined on input line 64407. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 585 undefined on input line 64422. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 585 undefined on input line 64422. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 585 undefined on input line 64437. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 585 undefined on input line 64437. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsteps' on page 585 undefined on input line 64455. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsteps' on page 585 undefi ned on input line 64455. [585] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 586 undefined on input line 64479. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 586 undefined on input line 64479. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .create_context' on page 586 undefined on input line 64488. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.creat e_context' on page 586 undefined on input line 64488. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .Context' on page 586 undefined on input line 64488. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Conte xt' on page 586 undefined on input line 64488. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .Context' on page 586 undefined on input line 64517. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Conte xt' on page 586 undefined on input line 64517. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .Context' on page 586 undefined on input line 64532. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Conte xt' on page 586 undefined on input line 64532. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDArgs' on page 586 undefined on input line 64532. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDArg s' on page 586 undefined on input line 64532. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDArgs' on page 586 undefined on input line 64557. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDArg s' on page 586 undefined on input line 64557. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDArgs' on page 586 undefined on input line 64572. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDArg s' on page 586 undefined on input line 64572. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDSession' on page 586 undefined on input line 64597. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 586 undefined on input line 64597. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDSession' on page 586 undefined on input line 64612. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 586 undefined on input line 64612. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDSystem' on page 586 undefined on input line 64637. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSys tem' on page 586 undefined on input line 64637. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .Context' on page 586 undefined on input line 64637. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Conte xt' on page 586 undefined on input line 64637. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .MDSession' on page 586 undefined on input line 64637. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 586 undefined on input line 64637. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 586 undefined on input line 64662. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 586 undefined on input line 64662. [586] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 587 undefined on input line 64734. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 587 undefined on input line 64734. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 587 undefined on input line 64734. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 587 undefined on input line 64734. [587] Chapter 7. [588] [589] [590] [591] Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool [592] [593] [594] Chapter 8. [595] LaTeX Warning: Hyper reference `dev-manual/testutils:gmx-make-new-tests' on pag e 596 undefined on input line 65499. LaTeX Warning: Reference `dev-manual/testutils:gmx-make-new-tests' on page 596 undefined on input line 65499. LaTeX Warning: Hyper reference `dev-manual/gitlab-ci::doc' on page 596 undefine d on input line 65505. LaTeX Warning: Reference `dev-manual/gitlab-ci::doc' on page 596 undefined on i nput line 65505. LaTeX Warning: Hyper reference `user-guide/mdp-options::doc' on page 596 undefi ned on input line 65528. LaTeX Warning: Reference `user-guide/mdp-options::doc' on page 596 undefined on input line 65528. LaTeX Warning: Hyper reference `reference-manual/file-formats:tpr' on page 596 undefined on input line 65529. LaTeX Warning: Reference `reference-manual/file-formats:tpr' on page 596 undefi ned on input line 65529. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 596 und efined on input line 65533. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 596 undefined on input line 65533. LaTeX Warning: Hyper reference `dev-manual/style::doc' on page 596 undefined on input line 65582. LaTeX Warning: Reference `dev-manual/style::doc' on page 596 undefined on input line 65582. LaTeX Warning: Hyper reference `dev-manual/formatting:code-formatting' on page 596 undefined on input line 65582. LaTeX Warning: Reference `dev-manual/formatting:code-formatting' on page 596 un defined on input line 65582. LaTeX Warning: Hyper reference `dev-manual/code-formatting:gmx-codeformatting' on page 596 undefined on input line 65585. LaTeX Warning: Reference `dev-manual/code-formatting:gmx-codeformatting' on pag e 596 undefined on input line 65585. [596] LaTeX Warning: Hyper reference `dev-manual/doxygen::doc' on page 597 undefined on input line 65590. LaTeX Warning: Reference `dev-manual/doxygen::doc' on page 597 undefined on inp ut line 65590. LaTeX Warning: Hyper reference `dev-manual/commitstyle:code-commitstyle' on pag e 597 undefined on input line 65596. LaTeX Warning: Reference `dev-manual/commitstyle:code-commitstyle' on page 597 undefined on input line 65596. LaTeX Warning: Hyper reference `dev-manual/change-management::doc' on page 597 undefined on input line 65605. LaTeX Warning: Reference `dev-manual/change-management::doc' on page 597 undefi ned on input line 65605. LaTeX Warning: Hyper reference `dev-manual/change-management::doc' on page 597 undefined on input line 65609. LaTeX Warning: Reference `dev-manual/change-management::doc' on page 597 undefi ned on input line 65609. LaTeX Warning: Hyper reference `user-guide/deprecation-policy:deprecation-polic y' on page 597 undefined on input line 65666. LaTeX Warning: Reference `user-guide/deprecation-policy:deprecation-policy' on page 597 undefined on input line 65666. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 597 undefined on input line 65669. LaTeX Warning: Reference `release-notes/index:release-notes' on page 597 undefi ned on input line 65669. LaTeX Warning: Hyper reference `api/index::doc' on page 597 undefined on input line 65693. LaTeX Warning: Reference `api/index::doc' on page 597 undefined on input line 6 5693. [597] LaTeX Warning: Hyper reference `dev-manual/build-system::doc' on page 598 undef ined on input line 65701. LaTeX Warning: Reference `dev-manual/build-system::doc' on page 598 undefined o n input line 65701. LaTeX Warning: Hyper reference `dev-manual/overview:dev-doc-layout' on page 598 undefined on input line 65707. LaTeX Warning: Reference `dev-manual/overview:dev-doc-layout' on page 598 undef ined on input line 65707. LaTeX Warning: Hyper reference `dev-manual/overview:dev-source-layout' on page 598 undefined on input line 65724. LaTeX Warning: Reference `dev-manual/overview:dev-source-layout' on page 598 un defined on input line 65724. LaTeX Warning: Hyper reference `api/index::doc' on page 598 undefined on input line 65745. LaTeX Warning: Reference `api/index::doc' on page 598 undefined on input line 6 5745. LaTeX Warning: Hyper reference `nblib/index::doc' on page 598 undefined on inpu t line 65747. LaTeX Warning: Reference `nblib/index::doc' on page 598 undefined on input line 65747. LaTeX Warning: Hyper reference `dev-manual/build-system::doc' on page 598 undef ined on input line 65756. LaTeX Warning: Reference `dev-manual/build-system::doc' on page 598 undefined o n input line 65756. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 598 undefine d on input line 65762. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 598 undefined on i nput line 65762. pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [598] LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 599 undefine d on input line 65789. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 599 undefined on i nput line 65789. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 599 undefine d on input line 65794. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 599 undefined on i nput line 65794. LaTeX Warning: Hyper reference `dev-manual/build-system::doc' on page 599 undef ined on input line 65803. LaTeX Warning: Reference `dev-manual/build-system::doc' on page 599 undefined o n input line 65803. [599 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] LaTeX Warning: Hyper reference `dev-manual/naming::doc' on page 600 undefined o n input line 65883. LaTeX Warning: Reference `dev-manual/naming::doc' on page 600 undefined on inpu t line 65883. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 600 undefine d on input line 65889. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 600 undefined on i nput line 65889. LaTeX Warning: Hyper reference `dev-manual/build-system::doc' on page 600 undef ined on input line 65899. LaTeX Warning: Reference `dev-manual/build-system::doc' on page 600 undefined o n input line 65899. [600] LaTeX Warning: Hyper reference `dev-manual/index:dev-guide' on page 601 undefin ed on input line 65963. LaTeX Warning: Reference `dev-manual/index:dev-guide' on page 601 undefined on input line 65963. LaTeX Warning: Hyper reference `dev-manual/doxygen::doc' on page 601 undefined on input line 65972. LaTeX Warning: Reference `dev-manual/doxygen::doc' on page 601 undefined on inp ut line 65972. [601] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 602 und efined on input line 66102. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 602 undefined on input line 66102. [602] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_SKIP_DEFAULT_ CFLAGS' on page 603 undefined on input line 66224. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_SKIP_DEFAULT_CFLAGS ' on page 603 undefined on input line 66224. [603] LaTeX Warning: Hyper reference `user-guide/mdrun-performance::doc' on page 604 undefined on input line 66326. LaTeX Warning: Reference `user-guide/mdrun-performance::doc' on page 604 undefi ned on input line 66326. LaTeX Warning: Hyper reference `dev-manual/relocatable-binaries::doc' on page 6 04 undefined on input line 66366. LaTeX Warning: Reference `dev-manual/relocatable-binaries::doc' on page 604 und efined on input line 66366. LaTeX Warning: Hyper reference `reference-manual/definitions::doc' on page 604 undefined on input line 66384. LaTeX Warning: Reference `reference-manual/definitions::doc' on page 604 undefi ned on input line 66384. LaTeX Warning: Hyper reference `install-guide/index:gmx-gpu-support' on page 60 4 undefined on input line 66486. LaTeX Warning: Reference `install-guide/index:gmx-gpu-support' on page 604 unde fined on input line 66486. LaTeX Warning: Hyper reference `install-guide/index:gmx-gpu-support' on page 60 4 undefined on input line 66500. LaTeX Warning: Reference `install-guide/index:gmx-gpu-support' on page 604 unde fined on input line 66500. [604] LaTeX Warning: Hyper reference `dev-manual/relocatable-binaries::doc' on page 6 05 undefined on input line 66528. LaTeX Warning: Reference `dev-manual/relocatable-binaries::doc' on page 605 und efined on input line 66528. LaTeX Warning: Hyper reference `install-guide/index:mpi-support' on page 605 un defined on input line 66556. LaTeX Warning: Reference `install-guide/index:mpi-support' on page 605 undefine d on input line 66556. LaTeX Warning: Hyper reference `install-guide/index:gmx-simd-support' on page 6 05 undefined on input line 66597. LaTeX Warning: Reference `install-guide/index:gmx-simd-support' on page 605 und efined on input line 66597. [605] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_UNITTES TS' on page 606 undefined on input line 66762. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_UNITTESTS' on page 606 undefined on input line 66762. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_COMPILER_WARN INGS' on page 606 undefined on input line 66764. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_COMPILER_WARNINGS' on page 606 undefined on input line 66764. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_ENABLE_CCACHE ' on page 606 undefined on input line 66801. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_ENABLE_CCACHE' on p age 606 undefined on input line 66801. LaTeX Warning: Hyper reference `nblib/index:nblib' on page 606 undefined on inp ut line 66835. LaTeX Warning: Reference `nblib/index:nblib' on page 606 undefined on input lin e 66835. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_DEVELOPER_BUI LD' on page 606 undefined on input line 66903. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_DEVELOPER_BUILD' on page 606 undefined on input line 66903. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-BUILD_TESTING' on page 606 undefined on input line 66906. LaTeX Warning: Reference `dev-manual/build-system:cmake-BUILD_TESTING' on page 606 undefined on input line 66906. [606] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-REGRESSIONTEST_PA TH' on page 607 undefined on input line 66937. LaTeX Warning: Reference `dev-manual/build-system:cmake-REGRESSIONTEST_PATH' on page 607 undefined on input line 66937. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 607 undefine d on input line 66996. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 607 undefined on i nput line 66996. LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 607 undefined on input line 67005. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 607 undefined on inp ut line 67005. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' o n page 607 undefined on input line 67011. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' on page 607 undefined on input line 67011. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' o n page 607 undefined on input line 67012. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' on page 607 undefined on input line 67012. LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 607 undefined on input line 67020. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 607 undefined on inp ut line 67020. LaTeX Warning: Hyper reference `dev-manual/doxygen::doc' on page 607 undefined on input line 67028. LaTeX Warning: Reference `dev-manual/doxygen::doc' on page 607 undefined on inp ut line 67028. [607] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' o n page 608 undefined on input line 67053. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' on page 608 undefined on input line 67053. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_MANUAL' on page 608 undefined on input line 67060. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_MANUAL' on pa ge 608 undefined on input line 67060. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 608 undefine d on input line 67072. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 608 undefined on i nput line 67072. LaTeX Warning: Hyper reference `dev-manual/testutils::doc' on page 608 undefine d on input line 67077. LaTeX Warning: Reference `dev-manual/testutils::doc' on page 608 undefined on i nput line 67077. [608] LaTeX Warning: Hyper reference `dev-manual/code-formatting:gmx-codeformatting' on page 609 undefined on input line 67193. LaTeX Warning: Reference `dev-manual/code-formatting:gmx-codeformatting' on pag e 609 undefined on input line 67193. LaTeX Warning: Hyper reference `dev-manual/reportstyle::doc' on page 609 undefi ned on input line 67223. LaTeX Warning: Reference `dev-manual/reportstyle::doc' on page 609 undefined on input line 67223. [609] LaTeX Warning: Hyper reference `dev-manual/change-management:code-review' on pa ge 610 undefined on input line 67268. LaTeX Warning: Reference `dev-manual/change-management:code-review' on page 610 undefined on input line 67268. LaTeX Warning: Hyper reference `dev-manual/change-management:status-label-guide lines' on page 610 undefined on input line 67333. LaTeX Warning: Reference `dev-manual/change-management:status-label-guidelines' on page 610 undefined on input line 67333. [610] LaTeX Warning: Hyper reference `dev-manual/style:style-guidelines' on page 611 undefined on input line 67394. LaTeX Warning: Reference `dev-manual/style:style-guidelines' on page 611 undefi ned on input line 67394. LaTeX Warning: Hyper reference `dev-manual/reportstyle:issue-workflow' on page 611 undefined on input line 67444. LaTeX Warning: Reference `dev-manual/reportstyle:issue-workflow' on page 611 un defined on input line 67444. LaTeX Warning: Hyper reference `dev-manual/change-management:merge-request-stat us' on page 611 undefined on input line 67448. LaTeX Warning: Reference `dev-manual/change-management:merge-request-status' on page 611 undefined on input line 67448. [611] LaTeX Warning: Hyper reference `dev-manual/reportstyle:issue-workflow' on page 612 undefined on input line 67511. LaTeX Warning: Reference `dev-manual/reportstyle:issue-workflow' on page 612 un defined on input line 67511. [612] [613] [614] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 615 undefined on input line 67920. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 615 undef ined on input line 67920. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 615 u ndefined on input line 67920. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 615 undefin ed on input line 67920. [615] Underfull \hbox (badness 10000) in paragraph at lines 68023--68029 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [616] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_MANUAL' on page 617 undefined on input line 68119. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_MANUAL' on pa ge 617 undefined on input line 68119. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' o n page 617 undefined on input line 68126. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_BUILD_HELP' on page 617 undefined on input line 68126. LaTeX Warning: Hyper reference `dev-manual/doxygen::doc' on page 617 undefined on input line 68196. LaTeX Warning: Reference `dev-manual/doxygen::doc' on page 617 undefined on inp ut line 68196. [617] LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 618 undefined on input line 68220. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 618 undefined on inp ut line 68220. LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 618 undefined on input line 68229. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 618 undefined on inp ut line 68229. [618] LaTeX Warning: Hyper reference `dev-manual/code-formatting::doc' on page 619 un defined on input line 68353. LaTeX Warning: Reference `dev-manual/code-formatting::doc' on page 619 undefine d on input line 68353. [619] LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 620 undefined on input line 68502. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 620 undefined on inp ut line 68502. [620] [621] [622] [623] [624] LaTeX Warning: Hyper reference `dev-manual/error-handling:error-handling' on pa ge 625 undefined on input line 69134. LaTeX Warning: Reference `dev-manual/error-handling:error-handling' on page 625 undefined on input line 69134. Underfull \hbox (badness 6575) in paragraph at lines 69147--69153 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [625] LaTeX Warning: Hyper reference `user-guide/terminology:blowing-up' on page 626 undefined on input line 69275. LaTeX Warning: Reference `user-guide/terminology:blowing-up' on page 626 undefi ned on input line 69275. LaTeX Warning: Hyper reference `dev-manual/formatting:code-formatting' on page 626 undefined on input line 69315. LaTeX Warning: Reference `dev-manual/formatting:code-formatting' on page 626 un defined on input line 69315. LaTeX Warning: Hyper reference `dev-manual/commitstyle:code-commitstyle' on pag e 626 undefined on input line 69315. LaTeX Warning: Reference `dev-manual/commitstyle:code-commitstyle' on page 626 undefined on input line 69315. [626] LaTeX Warning: Hyper reference `dev-manual/contribute::doc' on page 627 undefin ed on input line 69321. LaTeX Warning: Reference `dev-manual/contribute::doc' on page 627 undefined on input line 69321. LaTeX Warning: Hyper reference `dev-manual/style:style-guidelines' on page 627 undefined on input line 69389. LaTeX Warning: Reference `dev-manual/style:style-guidelines' on page 627 undefi ned on input line 69389. [627 <./redmine-states.png>] [628] [629] LaTeX Warning: Hyper reference `dev-manual/language-features:implementing-excep tions' on page 630 undefined on input line 69705. LaTeX Warning: Reference `dev-manual/language-features:implementing-exceptions' on page 630 undefined on input line 69705. LaTeX Warning: Hyper reference `dev-manual/overview:dev-doc-layout' on page 630 undefined on input line 69725. LaTeX Warning: Reference `dev-manual/overview:dev-doc-layout' on page 630 undef ined on input line 69725. [630] [631] LaTeX Warning: Hyper reference `dev-manual/gmxtree::doc' on page 632 undefined on input line 69935. LaTeX Warning: Reference `dev-manual/gmxtree::doc' on page 632 undefined on inp ut line 69935. [632] LaTeX Warning: Hyper reference `dev-manual/overview:dev-source-layout' on page 633 undefined on input line 69982. LaTeX Warning: Reference `dev-manual/overview:dev-source-layout' on page 633 un defined on input line 69982. LaTeX Warning: Hyper reference `dev-manual/overview:dev-doc-layout' on page 633 undefined on input line 70046. LaTeX Warning: Reference `dev-manual/overview:dev-doc-layout' on page 633 undef ined on input line 70046. [633] [634] Overfull \vbox (2.30272pt too high) detected at line 70296 [635] [636] [637] Overfull \vbox (1.24654pt too high) detected at line 70499 [638] Underfull \vbox (badness 10000) detected at line 70499 Underfull \vbox (badness 10000) detected at line 70499 [639] [640] [641] LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:containers' on page 642 un defined on input line 70687. LaTeX Warning: Reference `dev-manual/gitlab-ci:containers' on page 642 undefine d on input line 70687. LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:gitlab-ci-tools' on page 6 42 undefined on input line 70689. LaTeX Warning: Reference `dev-manual/gitlab-ci:gitlab-ci-tools' on page 642 und efined on input line 70689. [642] LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:containers' on page 643 un defined on input line 70740. LaTeX Warning: Reference `dev-manual/gitlab-ci:containers' on page 643 undefine d on input line 70740. LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:variables' on page 643 und efined on input line 70782. LaTeX Warning: Reference `dev-manual/gitlab-ci:variables' on page 643 undefined on input line 70782. LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:trigger-post-merge' on pag e 643 undefined on input line 70817. LaTeX Warning: Reference `dev-manual/gitlab-ci:trigger-post-merge' on page 643 undefined on input line 70817. [643] [644] LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:containers' on page 645 un defined on input line 70945. LaTeX Warning: Reference `dev-manual/gitlab-ci:containers' on page 645 undefine d on input line 70945. [645] LaTeX Warning: Hyper reference `dev-manual/gitlab-ci::doc' on page 646 undefine d on input line 71090. LaTeX Warning: Reference `dev-manual/gitlab-ci::doc' on page 646 undefined on i nput line 71090. LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:utility.image_name' on pag e 646 undefined on input line 71091. LaTeX Warning: Reference `dev-manual/gitlab-ci:utility.image_name' on page 646 undefined on input line 71091. [646] [647] LaTeX Warning: Hyper reference `dev-manual/gitlab-ci:module-scripted_gmx_docker _builds' on page 648 undefined on input line 71342. LaTeX Warning: Reference `dev-manual/gitlab-ci:module-scripted_gmx_docker_build s' on page 648 undefined on input line 71342. [648] [649] [650] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. [651] [652] LaTeX Warning: Hyper reference `dev-manual/doxygen::doc' on page 653 undefined on input line 71968. LaTeX Warning: Reference `dev-manual/doxygen::doc' on page 653 undefined on inp ut line 71968. [653] [654] LaTeX Warning: Hyper reference `dev-manual/formatting::doc' on page 655 undefin ed on input line 72228. LaTeX Warning: Reference `dev-manual/formatting::doc' on page 655 undefined on input line 72228. LaTeX Warning: Hyper reference `dev-manual/includestyle::doc' on page 655 undef ined on input line 72229. LaTeX Warning: Reference `dev-manual/includestyle::doc' on page 655 undefined o n input line 72229. [655] [656] [657] [658] [659] LaTeX Warning: Hyper reference `dev-manual/overview:dev-source-layout' on page 660 undefined on input line 72804. LaTeX Warning: Reference `dev-manual/overview:dev-source-layout' on page 660 un defined on input line 72804. [660] [661] [662] [663] [664] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 665 und efined on input line 73360. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 665 undefined on input line 73360. [665] Chapter 9. [666] Chapter 10. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 667 undefined on input line 73421. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 667 undefined on input line 73421. LaTeX Warning: Hyper reference `api/gmxlibs:cmake-Gromacs-libgromacs' on page 6 67 undefined on input line 73432. LaTeX Warning: Reference `api/gmxlibs:cmake-Gromacs-libgromacs' on page 667 und efined on input line 73432. LaTeX Warning: Hyper reference `api/gmxlibs:cmake-GROMACS_SUFFIX' on page 667 u ndefined on input line 73464. LaTeX Warning: Reference `api/gmxlibs:cmake-GROMACS_SUFFIX' on page 667 undefin ed on input line 73464. Underfull \hbox (badness 10000) in paragraph at lines 73462--73466 \T1/ptm/m/n/10 (page []) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share/cm ake/gromacs$GROMACS_-SUFFIX/ LaTeX Warning: Hyper reference `api/gmxlibs:gromacs_check_compiler' on page 667 undefined on input line 73475. LaTeX Warning: Reference `api/gmxlibs:gromacs_check_compiler' on page 667 undef ined on input line 73475. [667] LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 undefined on input line 73530. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 un defined on input line 73530. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_DOUBLE' on pa ge 668 undefined on input line 73538. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_DOUBLE' on page 668 undefined on input line 73538. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 undefined on input line 73538. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 un defined on input line 73538. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMXAPI' on page 6 68 undefined on input line 73542. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMXAPI' on page 668 und efined on input line 73542. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_DOUBLE' on pa ge 668 undefined on input line 73560. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_DOUBLE' on page 668 undefined on input line 73560. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 undefined on input line 73560. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_MPI' on page 668 un defined on input line 73560. [668] LaTeX Warning: Hyper reference `api/gmxlibs:cmake-GROMACS_SUFFIX' on page 669 u ndefined on input line 73626. LaTeX Warning: Reference `api/gmxlibs:cmake-GROMACS_SUFFIX' on page 669 undefin ed on input line 73626. [669] LaTeX Warning: Hyper reference `api/gmxlibs::doc' on page 670 undefined on inpu t line 73820. LaTeX Warning: Reference `api/gmxlibs::doc' on page 670 undefined on input line 73820. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMXAPI' on page 6 70 undefined on input line 73824. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMXAPI' on page 670 und efined on input line 73824. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_INSTALL_LEGAC Y_API' on page 670 undefined on input line 73831. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_INSTALL_LEGACY_API' on page 670 undefined on input line 73831. Underfull \hbox (badness 7504) in paragraph at lines 73829--73833 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by \T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API LaTeX Warning: Hyper reference `nblib/index:nblib' on page 670 undefined on inp ut line 73840. LaTeX Warning: Reference `nblib/index:nblib' on page 670 undefined on input lin e 73840. LaTeX Warning: Hyper reference `dev-manual/build-system:cmake-GMX_INSTALL_NBLIB _API' on page 670 undefined on input line 73840. LaTeX Warning: Reference `dev-manual/build-system:cmake-GMX_INSTALL_NBLIB_API' on page 670 undefined on input line 73840. [670] Chapter 11. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-counts' on page 671 undefined on input line 73921. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-counts' on pag e 671 undefined on input line 73921. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-wl-histogram-co unts' on page 671 undefined on input line 73921. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-wl-histogram-counts' on page 671 undefined on input line 73921. [671] LaTeX Warning: Hyper reference `reference-manual/special/plumed:plumed' on page 672 undefined on input line 73949. LaTeX Warning: Reference `reference-manual/special/plumed:plumed' on page 672 u ndefined on input line 73949. LaTeX Warning: Hyper reference `reference-manual/special/nnpot:nnpot' on page 6 72 undefined on input line 73974. LaTeX Warning: Reference `reference-manual/special/nnpot:nnpot' on page 672 und efined on input line 73974. [672] LaTeX Warning: Hyper reference `reference-manual/file-formats:gro' on page 673 undefined on input line 74105. LaTeX Warning: Reference `reference-manual/file-formats:gro' on page 673 undefi ned on input line 74105. [673] [674] [675] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-epsilon-r' on page 6 76 undefined on input line 74352. LaTeX Warning: Reference `user-guide/mdp-options:mdp-epsilon-r' on page 676 und efined on input line 74352. [676] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-lambda-counts' on page 677 undefined on input line 74430. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-lambda-counts' on pag e 677 undefined on input line 74430. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-init-wl-histogram-co unts' on page 677 undefined on input line 74430. LaTeX Warning: Reference `user-guide/mdp-options:mdp-init-wl-histogram-counts' on page 677 undefined on input line 74430. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 677 undefined on input line 74462. LaTeX Warning: Reference `release-notes/index:release-notes' on page 677 undefi ned on input line 74462. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 677 undefined on input line 74496. LaTeX Warning: Reference `release-notes/index:release-notes' on page 677 undefi ned on input line 74496. [677] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 678 undefined on input line 74581. LaTeX Warning: Reference `release-notes/index:release-notes' on page 678 undefi ned on input line 74581. [678] [679] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-couple-moltype' on p age 680 undefined on input line 74738. LaTeX Warning: Reference `user-guide/mdp-options:mdp-couple-moltype' on page 68 0 undefined on input line 74738. [680] [681] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 682 undefined on input line 74919. LaTeX Warning: Reference `release-notes/index:release-notes' on page 682 undefi ned on input line 74919. [682] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 683 un defined on input line 75027. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 683 undefine d on input line 75027. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 68 3 undefined on input line 75027. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 683 unde fined on input line 75027. [683] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rvdw' on page 684 un defined on input line 75088. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rvdw' on page 684 undefine d on input line 75088. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-rcoulomb' on page 68 4 undefined on input line 75088. LaTeX Warning: Reference `user-guide/mdp-options:mdp-rcoulomb' on page 684 unde fined on input line 75088. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 684 undefined on input line 75145. LaTeX Warning: Reference `release-notes/index:release-notes' on page 684 undefi ned on input line 75145. Underfull \hbox (badness 7168) in paragraph at lines 75153--75158 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 75311--75315 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 686 undefined on input line 75355. LaTeX Warning: Reference `release-notes/index:release-notes' on page 686 undefi ned on input line 75355. [686] [687] LaTeX Warning: Hyper reference `reference-manual/special/colvars:colvars' on pa ge 688 undefined on input line 75557. LaTeX Warning: Reference `reference-manual/special/colvars:colvars' on page 688 undefined on input line 75557. [688] [689] [690] [691] [692] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 693 undefined on input line 75983. LaTeX Warning: Reference `release-notes/index:release-notes' on page 693 undefi ned on input line 75983. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 693 undefined on input line 76007. LaTeX Warning: Reference `release-notes/index:release-notes' on page 693 undefi ned on input line 76007. [693] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 694 undefined on input line 76151. LaTeX Warning: Reference `release-notes/index:release-notes' on page 694 undefi ned on input line 76151. [694] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstlist' on page 695 undefined on input line 76186. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstlist' on page 695 undef ined on input line 76186. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 695 undefined on input line 76186. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 695 un defined on input line 76186. [695] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 696 undefined on input line 76258. LaTeX Warning: Reference `release-notes/index:release-notes' on page 696 undefi ned on input line 76258. [696] [697] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 698 undefined on input line 76504. LaTeX Warning: Reference `release-notes/index:release-notes' on page 698 undefi ned on input line 76504. [698] Underfull \hbox (badness 7722) in paragraph at lines 76624--76629 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [699] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.runtime .filtered_mpi_environ' on page 700 undefined on input line 76649. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.runtime.filte red_mpi_environ' on page 700 undefined on input line 76649. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 700 undefined on input line 76651. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 700 undefined on input line 76651. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun::doc' on page 700 undefine d on input line 76664. LaTeX Warning: Reference `onlinehelp/gmx-mdrun::doc' on page 700 undefined on i nput line 76664. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 700 undefined on input line 76671. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 700 undefined on input line 76671. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 700 undefined on input line 76680. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 700 undefined on input line 76680. [700] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 701 undefined on input line 76787. LaTeX Warning: Reference `release-notes/index:release-notes' on page 701 undefi ned on input line 76787. [701] [702] LaTeX Warning: Hyper reference `onlinehelp/gmx-dssp:gmx-dssp' on page 703 undef ined on input line 77039. LaTeX Warning: Reference `onlinehelp/gmx-dssp:gmx-dssp' on page 703 undefined o n input line 77039. [703] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.utility .join_path' on page 704 undefined on input line 77070. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.utility.join_ path' on page 704 undefined on input line 77070. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.simulat ion.mdrun.OutputDataProxy' on page 704 undefined on input line 77073. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.simulation.md run.OutputDataProxy' on page 704 undefined on input line 77073. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on page 704 undefined on input line 77089. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.mdrun' on pag e 704 undefined on input line 77089. LaTeX Warning: Hyper reference `install-guide/index:cufftmp-installation' on pa ge 704 undefined on input line 77132. LaTeX Warning: Reference `install-guide/index:cufftmp-installation' on page 704 undefined on input line 77132. LaTeX Warning: Hyper reference `install-guide/index:heffte-installation' on pag e 704 undefined on input line 77133. LaTeX Warning: Reference `install-guide/index:heffte-installation' on page 704 undefined on input line 77133. [704] [705] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 706 undefined on input line 77273. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 706 undefined on input line 77273. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 706 undefined on input line 77276. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 706 undefined on input line 77276. [706] [707] [708] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 709 undefined on input line 77568. LaTeX Warning: Reference `release-notes/index:release-notes' on page 709 undefi ned on input line 77568. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 709 undefined on input line 77618. LaTeX Warning: Reference `release-notes/index:release-notes' on page 709 undefi ned on input line 77618. [709] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 710 undefined on input line 77724. LaTeX Warning: Reference `release-notes/index:release-notes' on page 710 undefi ned on input line 77724. [710] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 711 und efined on input line 77759. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 711 undefined on input line 77759. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 711 undefin ed on input line 77804. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 711 undefined on input line 77804. LaTeX Warning: Hyper reference `onlinehelp/gmx-awh:gmx-awh' on page 711 undefin ed on input line 77806. LaTeX Warning: Reference `onlinehelp/gmx-awh:gmx-awh' on page 711 undefined on input line 77806. [711] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 712 undefined on input line 77846. LaTeX Warning: Reference `release-notes/index:release-notes' on page 712 undefi ned on input line 77846. [712] LaTeX Warning: Hyper reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 7 13 undefined on input line 77920. LaTeX Warning: Reference `onlinehelp/gmx-make_ndx:gmx-make-ndx' on page 713 und efined on input line 77920. LaTeX Warning: Hyper reference `onlinehelp/gmx-select:gmx-select' on page 713 u ndefined on input line 77920. LaTeX Warning: Reference `onlinehelp/gmx-select:gmx-select' on page 713 undefin ed on input line 77920. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 713 undefined on input line 77998. LaTeX Warning: Reference `release-notes/index:release-notes' on page 713 undefi ned on input line 77998. [713] LaTeX Warning: Hyper reference `user-guide/known-issues:gmx-users-known-issues' on page 714 undefined on input line 78075. LaTeX Warning: Reference `user-guide/known-issues:gmx-users-known-issues' on pa ge 714 undefined on input line 78075. [714] [715] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 716 undefined on input line 78205. LaTeX Warning: Reference `release-notes/index:release-notes' on page 716 undefi ned on input line 78205. [716] [717] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 718 undefined on input line 78401. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 718 undefined on input line 78401. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 718 undefined on input line 78401. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 718 undefined on input line 78401. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 718 undefined on input line 78407. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 718 undefined on input line 78407. [718] [719] LaTeX Warning: Hyper reference `reference-manual/references:refbeutler94' on pa ge 720 undefined on input line 78587. LaTeX Warning: Reference `reference-manual/references:refbeutler94' on page 720 undefined on input line 78587. LaTeX Warning: Hyper reference `reference-manual/references:refgapsys2012' on p age 720 undefined on input line 78587. LaTeX Warning: Reference `reference-manual/references:refgapsys2012' on page 72 0 undefined on input line 78587. [720] [721] [722] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 723 undefined on input line 78910. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 723 undefined on input line 78910. [723] [724] [725] [726] LaTeX Warning: Hyper reference `gmxapi/userguide/install::doc' on page 727 unde fined on input line 79325. LaTeX Warning: Reference `gmxapi/userguide/install::doc' on page 727 undefined on input line 79325. [727] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi. simulation' on page 728 undefined on input line 79434. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.simula tion' on page 728 undefined on input line 79434. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi.command line_operation' on page 728 undefined on input line 79438. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi.commandline_o peration' on page 728 undefined on input line 79438. [728] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 729 undefined on input line 79482. LaTeX Warning: Reference `release-notes/index:release-notes' on page 729 undefi ned on input line 79482. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 729 undefined on input line 79519. LaTeX Warning: Reference `release-notes/index:release-notes' on page 729 undefi ned on input line 79519. [729] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 730 undefined on input line 79637. LaTeX Warning: Reference `release-notes/index:release-notes' on page 730 undefi ned on input line 79637. [730] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 731 undefined on input line 79728. LaTeX Warning: Reference `release-notes/index:release-notes' on page 731 undefi ned on input line 79728. [731] [732] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 733 undefined on input line 79865. LaTeX Warning: Reference `release-notes/index:release-notes' on page 733 undefi ned on input line 79865. [733] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 734 undefined on input line 80016. LaTeX Warning: Reference `release-notes/index:release-notes' on page 734 undefi ned on input line 80016. [734] [735] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 736 undefined on input line 80165. LaTeX Warning: Reference `release-notes/index:release-notes' on page 736 undefi ned on input line 80165. [736] [737] [738] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 739 u ndefined on input line 80437. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 739 undefin ed on input line 80437. [739] [740] [741] [742] [743] [744] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 745 undefined on input line 81084. LaTeX Warning: Reference `release-notes/index:release-notes' on page 745 undefi ned on input line 81084. [745] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pcoupl-MTTK' o n page 746 undefined on input line 81134. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pcoupl-MTTK' on page 746 undefined on input line 81134. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-tcoupl-nose-ho over' on page 746 undefined on input line 81134. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-tcoupl-nose-hoover' on page 746 undefined on input line 81134. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-tcoupl-nose-ho over' on page 746 undefined on input line 81150. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-tcoupl-nose-hoover' on page 746 undefined on input line 81150. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-pcoupl-MTTK' o n page 746 undefined on input line 81167. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-pcoupl-MTTK' on page 746 undefined on input line 81167. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-tcoupl-nose-ho over' on page 746 undefined on input line 81167. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-tcoupl-nose-hoover' on page 746 undefined on input line 81167. [746] [747] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 748 undefined on input line 81278. LaTeX Warning: Reference `release-notes/index:release-notes' on page 748 undefi ned on input line 81278. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 748 u ndefined on input line 81353. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 748 undefin ed on input line 81353. [748] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 749 undefined on input line 81473. LaTeX Warning: Reference `release-notes/index:release-notes' on page 749 undefi ned on input line 81473. [749] [750] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 751 undefined on input line 81579. LaTeX Warning: Reference `release-notes/index:release-notes' on page 751 undefi ned on input line 81579. [751] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 752 undefined on input line 81693. LaTeX Warning: Reference `release-notes/index:release-notes' on page 752 undefi ned on input line 81693. [752] [753] [754] LaTeX Warning: Hyper reference `gmxapi/index:gmxapi' on page 755 undefined on i nput line 82006. LaTeX Warning: Reference `gmxapi/index:gmxapi' on page 755 undefined on input l ine 82006. [755] LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-trj:gmx-convert-trj' on page 756 undefined on input line 82133. LaTeX Warning: Reference `onlinehelp/gmx-convert-trj:gmx-convert-trj' on page 7 56 undefined on input line 82133. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 756 undefined on input line 82134. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 756 undef ined on input line 82134. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 756 undefined on input line 82138. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 756 undefi ned on input line 82138. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 756 undefined on input line 82139. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 756 undef ined on input line 82139. [756] LaTeX Warning: Hyper reference `onlinehelp/gmx-cluster:gmx-cluster' on page 757 undefined on input line 82147. LaTeX Warning: Reference `onlinehelp/gmx-cluster:gmx-cluster' on page 757 undef ined on input line 82147. LaTeX Warning: Hyper reference `onlinehelp/gmx-extract-cluster:gmx-extract-clus ter' on page 757 undefined on input line 82147. LaTeX Warning: Reference `onlinehelp/gmx-extract-cluster:gmx-extract-cluster' o n page 757 undefined on input line 82147. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 757 undefined on input line 82149. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 757 undef ined on input line 82149. [757] [758] [759] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 760 undefined on input line 82483. LaTeX Warning: Reference `release-notes/index:release-notes' on page 760 undefi ned on input line 82483. [760] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 761 undefined on input line 82559. LaTeX Warning: Reference `release-notes/index:release-notes' on page 761 undefi ned on input line 82559. [761] [762] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 763 undefined on input line 82733. LaTeX Warning: Reference `release-notes/index:release-notes' on page 763 undefi ned on input line 82733. [763] [764] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 765 undefined on input line 82914. LaTeX Warning: Reference `release-notes/index:release-notes' on page 765 undefi ned on input line 82914. LaTeX Warning: Hyper reference `onlinehelp/gmx-hbond:gmx-hbond' on page 765 und efined on input line 82995. LaTeX Warning: Reference `onlinehelp/gmx-hbond:gmx-hbond' on page 765 undefined on input line 82995. [765] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 766 undefined on input line 83051. LaTeX Warning: Reference `release-notes/index:release-notes' on page 766 undefi ned on input line 83051. [766] LaTeX Warning: Hyper reference `release-notes/2019/2019.1:release-notes-2019-1- gpu' on page 767 undefined on input line 83173. LaTeX Warning: Reference `release-notes/2019/2019.1:release-notes-2019-1-gpu' o n page 767 undefined on input line 83173. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 767 undefined on input line 83187. LaTeX Warning: Reference `release-notes/index:release-notes' on page 767 undefi ned on input line 83187. [767] [768] [769] LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 770 undefined on input line 83391. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 770 undefi ned on input line 83391. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 770 undefined on input line 83392. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 770 undefi ned on input line 83392. LaTeX Warning: Hyper reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 770 undefined on input line 83393. LaTeX Warning: Reference `onlinehelp/gmx-trjconv:gmx-trjconv' on page 770 undef ined on input line 83393. LaTeX Warning: Hyper reference `reference-manual/file-formats:ndx' on page 770 undefined on input line 83394. LaTeX Warning: Reference `reference-manual/file-formats:ndx' on page 770 undefi ned on input line 83394. LaTeX Warning: Hyper reference `reference-manual/file-formats:pdb' on page 770 undefined on input line 83395. LaTeX Warning: Reference `reference-manual/file-formats:pdb' on page 770 undefi ned on input line 83395. [770] [771] [772] [773] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 774 undefined on input line 83849. LaTeX Warning: Reference `release-notes/index:release-notes' on page 774 undefi ned on input line 83849. [774] LaTeX Warning: Hyper reference `release-notes/2018/2018.6:release-notes-2018-6- gpu' on page 775 undefined on input line 83888. LaTeX Warning: Reference `release-notes/2018/2018.6:release-notes-2018-6-gpu' o n page 775 undefined on input line 83888. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 775 undefined on input line 83901. LaTeX Warning: Reference `release-notes/index:release-notes' on page 775 undefi ned on input line 83901. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 775 undefined on input line 83963. LaTeX Warning: Reference `release-notes/index:release-notes' on page 775 undefi ned on input line 83963. [775] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 776 und efined on input line 84016. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 776 undefined on input line 84016. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 776 und efined on input line 84017. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 776 undefined on input line 84017. [776] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 777 undefined on input line 84093. LaTeX Warning: Reference `release-notes/index:release-notes' on page 777 undefi ned on input line 84093. [777] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 778 und efined on input line 84234. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 778 undefined on input line 84234. LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 778 undefined on input line 84256. LaTeX Warning: Reference `release-notes/index:release-notes' on page 778 undefi ned on input line 84256. [778] [779] [780] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 781 undefined on input line 84476. LaTeX Warning: Reference `release-notes/index:release-notes' on page 781 undefi ned on input line 84476. [781] [782] LaTeX Warning: Hyper reference `release-notes/index:release-notes' on page 783 undefined on input line 84707. LaTeX Warning: Reference `release-notes/index:release-notes' on page 783 undefi ned on input line 84707. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nsttcouple' on page 783 undefined on input line 84719. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nsttcouple' on page 783 un defined on input line 84719. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-nstpcouple' on page 783 undefined on input line 84719. LaTeX Warning: Reference `user-guide/mdp-options:mdp-nstpcouple' on page 783 un defined on input line 84719. [783] [784] [785] [786] [787] [788] LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 789 und efined on input line 85251. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 789 undefined on input line 85251. [789] LaTeX Warning: Hyper reference `onlinehelp/gmx-nmr:gmx-nmr' on page 790 undefin ed on input line 85384. LaTeX Warning: Reference `onlinehelp/gmx-nmr:gmx-nmr' on page 790 undefined on input line 85384. LaTeX Warning: Hyper reference `onlinehelp/gmx-energy:gmx-energy' on page 790 u ndefined on input line 85385. LaTeX Warning: Reference `onlinehelp/gmx-energy:gmx-energy' on page 790 undefin ed on input line 85385. LaTeX Warning: Hyper reference `onlinehelp/gmx-nmr:gmx-nmr' on page 790 undefin ed on input line 85391. LaTeX Warning: Reference `onlinehelp/gmx-nmr:gmx-nmr' on page 790 undefined on input line 85391. LaTeX Warning: Hyper reference `onlinehelp/gmx-traj:gmx-traj' on page 790 undef ined on input line 85399. LaTeX Warning: Reference `onlinehelp/gmx-traj:gmx-traj' on page 790 undefined o n input line 85399. [790] LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 791 undefined on input line 85463. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 791 undef ined on input line 85463. LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-cutoff-scheme- Verlet' on page 791 undefined on input line 85465. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-cutoff-scheme-Verlet ' on page 791 undefined on input line 85465. LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 791 u ndefined on input line 85471. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 791 undefin ed on input line 85471. [791] LaTeX Warning: Hyper reference `user-guide/mdp-options:mdp-value-coulombtype-PM E-User' on page 792 undefined on input line 85619. LaTeX Warning: Reference `user-guide/mdp-options:mdp-value-coulombtype-PME-User ' on page 792 undefined on input line 85619. [792] LaTeX Warning: Hyper reference `onlinehelp/gmx-grompp:gmx-grompp' on page 793 u ndefined on input line 85684. LaTeX Warning: Reference `onlinehelp/gmx-grompp:gmx-grompp' on page 793 undefin ed on input line 85684. LaTeX Warning: Hyper reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 793 undefined on input line 85706. LaTeX Warning: Reference `onlinehelp/gmx-pdb2gmx:gmx-pdb2gmx' on page 793 undef ined on input line 85706. [793] LaTeX Warning: Hyper reference `onlinehelp/gmx-solvate:gmx-solvate' on page 794 undefined on input line 85724. LaTeX Warning: Reference `onlinehelp/gmx-solvate:gmx-solvate' on page 794 undef ined on input line 85724. [794] [795] LaTeX Warning: Hyper reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 796 undefined on input line 85962. LaTeX Warning: Reference `onlinehelp/gmx-convert-tpr:gmx-convert-tpr' on page 7 96 undefined on input line 85962. LaTeX Warning: Hyper reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 796 und efined on input line 85991. LaTeX Warning: Reference `onlinehelp/gmx-mdrun:gmx-mdrun' on page 796 undefined on input line 85991. [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] Overfull \hbox (18.01631pt too wide) in paragraph at lines 87778--87781 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 87778--87781 [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 826 undefined on input line 88820. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi._gmxap i' on page 826 undefined on input line 88821. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi._loggi ng' on page 826 undefined on input line 88822. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.except ions' on page 826 undefined on input line 88823. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.runtim e' on page 826 undefined on input line 88824. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.simula tion' on page 826 undefined on input line 88825. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.utilit y' on page 826 undefined on input line 88826. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi.versio n' on page 826 undefined on input line 88827. LaTeX Warning: Reference `dev-manual/gitlab-ci:module-scripted_gmx_docker_build s' on page 826 undefined on input line 88830. LaTeX Warning: Reference `dev-manual/gitlab-ci:module-utility' on page 826 unde fined on input line 88833. [826] No file gromacs.ind. (./gromacs.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcit1000 mkdir: cannot create directory '././nonexistent': Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcit1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcit1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcit.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txitlod.mf Ok [48] [49] [53] [54] [56] [57] [50] [51] [52] [55]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txisuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txifract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tcit1000.tfm. Output written on tcit1000.600gf (128 characters, 19308 bytes). Transcript written on tcit1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcit1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `gromacs.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory '././nonexistent': Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory '././nonexistent': Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tctt1000.tfm. Output written on tctt1000.600gf (128 characters, 19540 bytes). Transcript written on tctt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt1000.600pk: successfully generated. < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (828 pages, 13335818 bytes). Transcript written on gromacs.log. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./gromacs.tex LaTeX2e <2024-11-01> patch level 1 L3 programming layer <2024-12-25> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (./sphinxpackagefootnote.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (./here.sty) (./picins.sty Option `picins' Version 3.0 Sep. 1992, TH Darmstadt/HRZ) (./underscore.sty) ==> First Aid for underscore.sty no longer applied! Expected: 2006/09/13 but found: 2001/10/12 so I'm assuming it got fixed. (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/dcolumn.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape.sty (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape-nometadata.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/lscape.sty))) Writing index file gromacs.idx (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) LaTeX Warning: Unused global option(s): [11]. (./gromacs.aux LaTeX Warning: Label `footnotemark.4' multiply defined. LaTeX Warning: Label `footnotemark.5' multiply defined. LaTeX Warning: Label `footnotemark.6' multiply defined. ) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./gromacs.out) (./gromacs.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc} <./gmx_falcon_blue.png>] (./gromacs.toc [1] [2] [3] [4] [5] [6] [7] [8]) [9] [1] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] Underfull \hbox (badness 5105) in paragraph at lines 303--311 \T1/pcr/m/n/10 CXX_-FLAGS\T1/ptm/m/n/10 . A clang com-piler is re-quired with v er-sion >=19. If you want to check which [4] [5] [6] [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 881--886 []\T1/ptm/m/n/10 Sup-port for this fea-ture in GRO-MACS is cur-rently en-abled by build-ing with NVSH-MEM Underfull \hbox (badness 10000) in paragraph at lines 881--886 \T1/ptm/m/n/10 sup-port (\T1/pcr/m/n/10 GMX_-NVSHMEM=ON\T1/ptm/m/n/10 ) and spe c-i-fy-ing the NVSH-MEM root di-rec-tory (\T1/pcr/m/n/10 NVSHMEM_- [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2092--2094 [][]\T1/pcr/m/n/10 DGMX_-FFT_-LIBRARY= []DFFTWF_-LIBRA RY=, but at most version <1.5> allowed [28] [29 <./graphviz-546f8676b043be7a824d2ab2320a5e60473f82fc.pdf>] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 4307--4313 \T1/ptm/m/n/10 Use a mul-ti-ple timing-stepping in-te-gra-tor to eval-u-ate som e forces, as spec-i-fied by [42] [43] [44] Underfull \hbox (badness 5862) in paragraph at lines 4833--4839 \T1/ptm/m/n/10 Gen-er-ate a pair list with buffer-ing. The buffer size is au-to -mat-i-cally set based on Underfull \hbox (badness 10000) in paragraph at lines 4882--4892 \T1/ptm/m/n/10 In-ter-val be-tween steps that up-date the neigh-bor list. When dy-nam-ics and [45] [46] [47] [48] [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 6013--6018 []\T1/ptm/m/n/10 The en-sem-ble tem-per-a-ture for the sys-tem. The in-put valu e is only used with [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 7792--7796 \T1/ptm/m/n/10 The name of the ex-ter-nal mod-ule that pro-vides the po-ten-tia l for the case where [59] Underfull \hbox (badness 7186) in paragraph at lines 7925--7929 \T1/ptm/m/n/10 As [][]\T1/pcr/m/sl/10 pull[]coord1[]geometry=angle[][] \T1/ptm/ m/n/10 (page 60[]) but the sec-ond vec-tor is given by Underfull \hbox (badness 10000) in paragraph at lines 7957--7963 \T1/ptm/m/n/10 Trans-forms other pull co-or-di-nates us-ing a math-e-mat-i-cal ex-pres-sion de-fined by [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 10885--10890 \T1/ptm/m/n/10 Con-trols the way that the tem-per-a-tures at in-ter-me-di-ate l amb-das are cal-cu-lated from the [74] [75] [76] [77] Overfull \hbox (39.0321pt too wide) in paragraph at lines 11741--11741 []\T1/pcr/b/n/10 density[]guided[]simulation[]gaussian[]transform[]spreading[]r ange[]in[]multiples[]of[]width| [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] Underfull \hbox (badness 6927) in paragraph at lines 14329--14333 []\T1/ptm/m/n/10 When us-ing a time-step of <=2.5 fs, use [][]\T1/pcr/m/sl/10 c onstraints=h[]bonds[][] \T1/ptm/m/n/10 (page 55[]) (and not [101] [102] [103] [104] [105] [106] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. [119] [120] [121] [122] [123] [124] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] Underfull \hbox (badness 10000) in paragraph at lines 27897--27900 []\T1/pcr/m/n/10 gmx rotacf []P 1 []nparm 2 []fft []n index []o rotacf[]x[]P1 [ ]fa expfit[]x[]P1 [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] Underfull \hbox (badness 10000) in paragraph at lines 29639--29641 []\T1/pcr/m/n/10 gmx trjconv []s a.tpr []f a.tng []o b.tng []boxcenter tric []u r compact []pbc [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Chapter 4. [321] [322] [323] [324] [325] [326] [327] [328] [329] Chapter 5. [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340 <./pbctric.pdf>] [341 <./rhododec.pdf> <./truncoct.pdf pdfTeX warning: /usr/bin/pdflatex (file ./truncoct.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [342] [343] [344] [345 <./maxwell.pdf>] [346]<> [347 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39411 ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [348 <./verlet-drift.pdf>] [349] [350 <./nstric.pdf>] [351 <./leapfrog.pdf>] [352 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.31 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39816 \end{equation} ] [353 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.33 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 ] [354] [355] [356] [357 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40283 ] [358 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [359] [360] [361] [362 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.63 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.65 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} ] [363 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} ] [364 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.69 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [365 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.41000 ] [366] [367] Package amsmath Warning: Foreign command \over; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 41176. [368 <./lincs.pdf>] [369] [370] [371] [372] [373 <./free1.pdf> <./free2.pdf pdfTeX warning: /usr/bin/pdflatex (file ./free2.pdf): PDF inclusion: multiple p dfs with page group included in a single page >] [374] [375] [376] [377] [378 <./dd-cells.pdf> <./dd-tric.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dd-tric.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [379 <./par-lincs2.pdf>] [380] [381 <./mpmd-pme.pdf>] [382 <./flowchart.pdf>] [383] [384 <./f-lj.pdf> <./f-bham.pdf pdfTeX warning: /usr/bin/pdflatex (file ./f-bham.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [385 <./vcrf.pdf>] [386] [387] [388 <./bstretch.pdf>] [389 <./f-morse.pdf>] [390 <./angle.pdf>] [391 <./fig-02.pdf>] [392] [393 <./ring-imp.pdf> <./subst-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./subst-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page > <./tetra-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./tetra-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [394 <./f-imps.pdf> <./f-dih.pdf>] [395 <./f-rbs.pdf>] [396] [397 <./fig-04.pdf>] [398] [399 <./f-pr.pdf>] [400 <./fbposres.pdf>] [401] [402 <./f-dr.pdf>] [403] [404] [405] [406] [407] [408 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} ] [409] [410 <./softcore.pdf>] [411] [412 <./gapsys-sc.pdf>] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45084. [413] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45108. [414] [415 <./chain.pdf>] pdfTeX warning: /usr/bin/pdflatex (file ./dummies.pdf): PDF inclusion: found PD F version <1.7>, but at most version <1.5> allowed [416 <./dummies.pdf>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45478. [417] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45600. [418] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. [419 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.27 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45729 <./vsite-4fdn.pdf>] [420] [421] [422] [423 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46108 \end{equation} ] [424 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} ] [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Underfull \vbox (badness 2368) detected at line 47468 [436] [437] [438] [439] [440] [441] Underfull \hbox (badness 10000) in paragraph at lines 48166--48169 []\T1/pcr/m/n/10 resA atomA nbondsA resB atomB nbondsB length newresA newresB [ atomI atomJ Overfull \hbox (10.25368pt too wide) in paragraph at lines 48373--48375 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 48386--48388 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 48402--48404 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48418--48420 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ [442] Underfull \hbox (badness 10000) in paragraph at lines 48468--48470 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 48481--48485 \T1/ptm/m/n/10 num-ber; residue [443] Underfull \hbox (badness 10000) in paragraph at lines 48619--48621 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 48622--48625 []|\T1/phv/m/n/10 num. Underfull \hbox (badness 10000) in paragraph at lines 48626--48629 []|\T1/phv/m/n/10 func. Underfull \hbox (badness 10000) in paragraph at lines 48633--48637 []|\T1/phv/m/n/10 use in Underfull \hbox (badness 10000) in paragraph at lines 48648--48650 []|\T1/phv/m/n/10 Topol-ogy file Overfull \hbox (35.51122pt too wide) in paragraph at lines 48720--48722 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Overfull \hbox (35.51122pt too wide) in paragraph at lines 48739--48741 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48748--48750 []|$\OML/cmm/m/it/10 b[]$ \T1/ptm/m/n/10 (nm); $\OML/cmm/m/it/10 D$ Overfull \hbox (35.51122pt too wide) in paragraph at lines 48758--48760 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48784--48786 []|\T1/ptm/m/n/10 har-monic Underfull \hbox (badness 10000) in paragraph at lines 48831--48833 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48854--48856 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48873--48875 []|\T1/ptm/m/n/10 low, up$[]$,$[]$ Underfull \hbox (badness 10000) in paragraph at lines 48880--48882 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48903--48905 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 6157) in paragraph at lines 48915--48917 []|\T1/ptm/m/n/10 fudge QQ (); Underfull \hbox (badness 10000) in paragraph at lines 48915--48917 \OML/cmm/m/it/10 q[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 q[]$ \T1/ptm/m/n/10 (e) , Underfull \hbox (badness 10000) in paragraph at lines 48915--48917 \OML/cmm/m/it/10 V$[][][][][][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48919--48921 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48931--48933 []|$\OML/cmm/m/it/10 q[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 q[]$ \T1/ptm/m/n/10 (e); Underfull \hbox (badness 10000) in paragraph at lines 48931--48933 \OML/cmm/m/it/10 V$[][][][][][][]\T1/ptm/m/n/10 ; Overfull \hbox (5.75829pt too wide) in paragraph at lines 48938--48940 []|\T1/pcr/m/n/10 angles[][][][][][][]| Overfull \hbox (5.75829pt too wide) in paragraph at lines 48957--48959 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48973--48975 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 10000) in paragraph at lines 48985--48987 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 48989--48991 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 6542) in paragraph at lines 49001--49003 []|$\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$ Overfull \hbox (5.75829pt too wide) in paragraph at lines 49008--49010 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \T1/ptm/m/n/10 mol$[]$rad$[]$); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 r[]$ \T1/ptm/m/n/10 (nm); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Overfull \hbox (5.75829pt too wide) in paragraph at lines 49027--49029 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49036--49038 []|$\OML/cmm/m/it/10 ^^R[]$ \T1/ptm/m/n/10 (deg); Underfull \hbox (badness 10000) in paragraph at lines 49052--49054 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 5592) in paragraph at lines 49071--49073 []|$\OML/cmm/m/it/10 a[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 []|\T1/ptm/m/n/10 Ryckaert- Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 \T1/ptm/m/n/10 Bellemans Underfull \hbox (badness 7888) in paragraph at lines 49146--49148 []|$\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 49153--49155 []|\T1/ptm/m/n/10 pe-ri-odic im- Underfull \hbox (badness 10000) in paragraph at lines 49172--49174 []|\T1/ptm/m/n/10 Fourier di-he- Underfull \hbox (badness 10000) in paragraph at lines 49203--49205 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 []|\T1/ptm/m/n/10 com-bined Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 \T1/ptm/m/n/10 bending-torsion Underfull \hbox (badness 10000) in paragraph at lines 49270--49272 []|\T1/ptm/m/n/10 one or more Overfull \hbox (35.75829pt too wide) in paragraph at lines 49277--49279 []|\T1/pcr/m/n/10 constraints[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49293--49295 []|\T1/ptm/m/n/10 con- Overfull \hbox (2.50536pt too wide) in paragraph at lines 49296--49298 []|\T1/pcr/m/n/10 constraints| Underfull \hbox (badness 10000) in paragraph at lines 49328--49330 []|\T1/ptm/m/n/10 1-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49331--49333 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49341--49343 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49344--49346 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49357--49359 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49360--49362 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49373--49375 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49376--49378 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49389--49391 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49392--49394 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49405--49407 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49408--49410 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49421--49423 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49424--49426 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49433--49435 []|$\OML/cmm/m/it/10 a$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 (); $\OML/cmm/m/it/10 c$ Underfull \hbox (badness 10000) in paragraph at lines 49437--49439 []|\T1/ptm/m/n/10 4-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49440--49442 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49456--49458 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49472--49474 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49488--49490 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49503--49505 []|\T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49506--49508 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 []|\T1/ptm/m/n/10 flat-bottomed Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 \T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49525--49527 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49538--49540 []|\T1/ptm/m/n/10 dis-tance re- Underfull \hbox (badness 10000) in paragraph at lines 49541--49543 []|\T1/pcr/m/n/10 distance_- Underfull \hbox (badness 10000) in paragraph at lines 49550--49552 \T1/ptm/m/n/10 up$[]$,$[]$ (nm); Underfull \hbox (badness 10000) in paragraph at lines 49554--49556 []|\T1/ptm/m/n/10 di-he-dral re- Underfull \hbox (badness 10000) in paragraph at lines 49557--49559 []|\T1/pcr/m/n/10 dihedral_- Underfull \hbox (badness 10000) in paragraph at lines 49573--49575 []|\T1/ptm/m/n/10 ori-en-ta-tion Overfull \hbox (14.50536pt too wide) in paragraph at lines 49576--49578 []|\T1/pcr/m/n/10 orientation_- Underfull \hbox (badness 10000) in paragraph at lines 49585--49587 \T1/ptm/m/n/10 (U); weight Underfull \hbox (badness 10000) in paragraph at lines 49592--49594 []|\T1/pcr/m/n/10 angle_- Underfull \hbox (badness 10000) in paragraph at lines 49608--49610 []|\T1/ptm/m/n/10 an-gle re-straint Underfull \hbox (badness 10000) in paragraph at lines 49611--49613 []|\T1/pcr/m/n/10 angle_- Overfull \hbox (8.50536pt too wide) in paragraph at lines 49611--49613 \T1/pcr/m/n/10 restraints_- [444] [445] [446 pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { }] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50222--50225 []\T1/phv/m/n/10 ex-pected Underfull \hbox (badness 10000) detected at line 50226 []\T1/phv/m/n/10 ex-pected [452] [453] [454] [455] [456] [457] [458] [459] [460 <./plotje.png>] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471 <./xvgr.png>] [472 <./lambda-values.pdf>] [473] [474 <./pull.pdf>] [475] [476 <./pullref.pdf>] [477 <./pulldirrel.pdf>] [478] [479] [480] [481 <./awh-traj.pdf> <./awh-invN.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-invN.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [482 <./awh-sampleweights.pdf> <./awh-pmfs.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-pmfs.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [483] [484] [485] [486] [487] [488 <./rotation.pdf>] [489 <./equipotential.pdf>] [490 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53629 \subsubsection{Radial Motion Potential} ] [491] [492 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.35 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53881 \end{equation} ] [493 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53968 \end{equation} <./gaussians.pdf>] Overfull \hbox (1.42029pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 pivot| Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 slab- Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 min- Overfull \hbox (2.21065pt too wide) in paragraph at lines 54578--54578 []$[]$| Overfull \hbox (1.2207pt too wide) in paragraph at lines 54578--54578 []$[]$\T1/phv/m/n/10 /ps| Overfull \hbox (1.25058pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 nm$[]$| Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/ptm/m/n/10 par-al-lel mo- [494] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... [495] [496] [497 <./field.pdf>] [498 <./compelsetup.pdf>] [499] [500] [501] [502 <./dumtypes.pdf> <./dumaro.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dumaro.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525 <./rdf.pdf>] [526 <./rdfO-O.pdf>] [527] [528] [529] [530 <./msdwater.pdf>] [531 <./dih-def.pdf> <./sgangle.pdf pdfTeX warning: /usr/bin/pdflatex (file ./sgangle.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [532 <./distm.pdf>] [533] [534] [535 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [536 <./phipsi.pdf>] [537 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [538] [539] [540 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58763 ...ecular shift (mol\sphinxhyphen{}shift)} ] [541] [542] [543 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 1}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59057 \end{equation} ] [544] [545 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... [546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59250 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61748--61751 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. [570] [571] [572] Overfull \vbox (1.4634pt too high) detected at line 62640 [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] [587] [588] Chapter 7. [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool [593] [594] [595] Chapter 8. [596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 68023--68029 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69147--69153 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [626] [627] [628 <./redmine-states.png>] [629] [630] [631] [632] [633] [634] [635] Overfull \vbox (2.30272pt too high) detected at line 70296 [636] [637] [638] Overfull \vbox (1.24654pt too high) detected at line 70499 [639] Underfull \vbox (badness 10000) detected at line 70499 Underfull \vbox (badness 10000) detected at line 70499 [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Chapter 9. [667] Chapter 10. Underfull \hbox (badness 10000) in paragraph at lines 73462--73466 \T1/ptm/m/n/10 (page 669[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73829--73833 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 7168) in paragraph at lines 75153--75158 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [685] [686] Underfull \hbox (badness 10000) in paragraph at lines 75311--75315 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 7722) in paragraph at lines 76624--76629 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Overfull \hbox (18.01631pt too wide) in paragraph at lines 87778--87781 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 87778--87781 [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] No file gromacs.ind. (./gromacs.aux) LaTeX Warning: There were multiply-defined labels. Package rerunfilecheck Warning: File `gromacs.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (837 pages, 13749096 bytes). Transcript written on gromacs.log. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./gromacs.tex LaTeX2e <2024-11-01> patch level 1 L3 programming layer <2024-12-25> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (./sphinxpackagefootnote.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (./here.sty) (./picins.sty Option `picins' Version 3.0 Sep. 1992, TH Darmstadt/HRZ) (./underscore.sty) ==> First Aid for underscore.sty no longer applied! Expected: 2006/09/13 but found: 2001/10/12 so I'm assuming it got fixed. (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/dcolumn.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape.sty (/usr/share/texlive/texmf-dist/tex/latex/pdflscape/pdflscape-nometadata.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/lscape.sty))) Writing index file gromacs.idx (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) LaTeX Warning: Unused global option(s): [11]. (./gromacs.aux LaTeX Warning: Label `footnotemark.4' multiply defined. LaTeX Warning: Label `footnotemark.5' multiply defined. LaTeX Warning: Label `footnotemark.6' multiply defined. ) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./gromacs.out) (./gromacs.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc} <./gmx_falcon_blue.png>] (./gromacs.toc [1] [2] [3] [4] [5] [6] [7] [8]) [9] [1] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] Underfull \hbox (badness 5105) in paragraph at lines 303--311 \T1/pcr/m/n/10 CXX_-FLAGS\T1/ptm/m/n/10 . A clang com-piler is re-quired with v er-sion >=19. If you want to check which [4] [5] [6] [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 881--886 []\T1/ptm/m/n/10 Sup-port for this fea-ture in GRO-MACS is cur-rently en-abled by build-ing with NVSH-MEM Underfull \hbox (badness 10000) in paragraph at lines 881--886 \T1/ptm/m/n/10 sup-port (\T1/pcr/m/n/10 GMX_-NVSHMEM=ON\T1/ptm/m/n/10 ) and spe c-i-fy-ing the NVSH-MEM root di-rec-tory (\T1/pcr/m/n/10 NVSHMEM_- [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2092--2094 [][]\T1/pcr/m/n/10 DGMX_-FFT_-LIBRARY= []DFFTWF_-LIBRA RY=, but at most version <1.5> allowed [28] [29 <./graphviz-546f8676b043be7a824d2ab2320a5e60473f82fc.pdf>] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 4307--4313 \T1/ptm/m/n/10 Use a mul-ti-ple timing-stepping in-te-gra-tor to eval-u-ate som e forces, as spec-i-fied by [42] [43] [44] Underfull \hbox (badness 5862) in paragraph at lines 4833--4839 \T1/ptm/m/n/10 Gen-er-ate a pair list with buffer-ing. The buffer size is au-to -mat-i-cally set based on Underfull \hbox (badness 10000) in paragraph at lines 4882--4892 \T1/ptm/m/n/10 In-ter-val be-tween steps that up-date the neigh-bor list. When dy-nam-ics and [45] [46] [47] [48] [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 6013--6018 []\T1/ptm/m/n/10 The en-sem-ble tem-per-a-ture for the sys-tem. The in-put valu e is only used with [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 7792--7796 \T1/ptm/m/n/10 The name of the ex-ter-nal mod-ule that pro-vides the po-ten-tia l for the case where [59] Underfull \hbox (badness 7186) in paragraph at lines 7925--7929 \T1/ptm/m/n/10 As [][]\T1/pcr/m/sl/10 pull[]coord1[]geometry=angle[][] \T1/ptm/ m/n/10 (page 60[]) but the sec-ond vec-tor is given by Underfull \hbox (badness 10000) in paragraph at lines 7957--7963 \T1/ptm/m/n/10 Trans-forms other pull co-or-di-nates us-ing a math-e-mat-i-cal ex-pres-sion de-fined by [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 10885--10890 \T1/ptm/m/n/10 Con-trols the way that the tem-per-a-tures at in-ter-me-di-ate l amb-das are cal-cu-lated from the [74] [75] [76] [77] Overfull \hbox (39.0321pt too wide) in paragraph at lines 11741--11741 []\T1/pcr/b/n/10 density[]guided[]simulation[]gaussian[]transform[]spreading[]r ange[]in[]multiples[]of[]width| [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] Underfull \hbox (badness 6927) in paragraph at lines 14329--14333 []\T1/ptm/m/n/10 When us-ing a time-step of <=2.5 fs, use [][]\T1/pcr/m/sl/10 c onstraints=h[]bonds[][] \T1/ptm/m/n/10 (page 55[]) (and not [101] [102] [103] [104] [105] [106] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 14921. [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 16092. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16105. [119] [120] [121] [122] [123] [124] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 16655. [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] Underfull \hbox (badness 10000) in paragraph at lines 27897--27900 []\T1/pcr/m/n/10 gmx rotacf []P 1 []nparm 2 []fft []n index []o rotacf[]x[]P1 [ ]fa expfit[]x[]P1 [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] Underfull \hbox (badness 10000) in paragraph at lines 29639--29641 []\T1/pcr/m/n/10 gmx trjconv []s a.tpr []f a.tng []o b.tng []boxcenter tric []u r compact []pbc [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31846. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31847. [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Chapter 4. [321] [322] [323] [324] [325] [326] [327] [328] [329] Chapter 5. [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340 <./pbctric.pdf>] [341 <./rhododec.pdf> <./truncoct.pdf pdfTeX warning: /usr/bin/pdflatex (file ./truncoct.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [342] [343] [344] [345 <./maxwell.pdf>] [346]<> [347 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39411 ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.18 }) has been already used, duplicate ignored \relax l.39422 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [348 <./verlet-drift.pdf>] [349] [350 <./nstric.pdf>] [351 <./leapfrog.pdf>] [352 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.31 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39816 \end{equation} ] [353 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.33 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.39918 ] [354] [355] [356] [357 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40283 ] [358 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40370 ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.48 }) has been already used, duplicate ignored \relax l.40396 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [359] [360] [361] [362 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.63 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.65 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40752 \end{equation} ] [363 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.66 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40786 \end{equation} ] [364 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.69 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.40872 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40875 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored \relax l.40959 \begin{equation} \label{equation:reference-manual/algorithms/molecula... [365 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.71 }) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.41000 ] [366] [367] Package amsmath Warning: Foreign command \over; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 41176. [368 <./lincs.pdf>] [369] [370] [371] [372] [373 <./free1.pdf> <./free2.pdf pdfTeX warning: /usr/bin/pdflatex (file ./free2.pdf): PDF inclusion: multiple p dfs with page group included in a single page >] [374] [375] [376] [377] [378 <./dd-cells.pdf> <./dd-tric.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dd-tric.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [379 <./par-lincs2.pdf>] [380] [381 <./mpmd-pme.pdf>] [382 <./flowchart.pdf>] [383] [384 <./f-lj.pdf> <./f-bham.pdf pdfTeX warning: /usr/bin/pdflatex (file ./f-bham.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [385 <./vcrf.pdf>] [386] [387] [388 <./bstretch.pdf>] [389 <./f-morse.pdf>] [390 <./angle.pdf>] [391 <./fig-02.pdf>] [392] [393 <./ring-imp.pdf> <./subst-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./subst-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page > <./tetra-im.pdf pdfTeX warning: /usr/bin/pdflatex (file ./tetra-im.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [394 <./f-imps.pdf> <./f-dih.pdf>] [395 <./f-rbs.pdf>] [396] [397 <./fig-04.pdf>] [398] [399 <./f-pr.pdf>] [400 <./fbposres.pdf>] [401] [402 <./f-dr.pdf>] [403] [404] [405] [406] [407] [408 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.23 0}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.44726 ...oulomb interaction with reaction field} ] [409] [410 <./softcore.pdf>] [411] [412 <./gapsys-sc.pdf>] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.24 4}) has been already used, duplicate ignored \relax l.45003 ...er-waals-interactions}}\begin{equation} \label{equation:reference-... Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45084. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45084. [413] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\partial' on input line 45108. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lambda' on input line 45108. [414] [415 <./chain.pdf>] pdfTeX warning: /usr/bin/pdflatex (file ./dummies.pdf): PDF inclusion: found PD F version <1.7>, but at most version <1.5> allowed [416 <./dummies.pdf>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45402. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45423. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45462. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45478. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45478. [417] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45520. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45600. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45600. [418] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@ifnextchar' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\spacefactor' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\@m' on input line 45639. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 45706. [419 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.27 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45729 <./vsite-4fdn.pdf>] [420] [421] [422] [423 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46108 \end{equation} ] [424 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} ] [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Underfull \vbox (badness 2368) detected at line 47468 [436] [437] [438] [439] [440] [441] Underfull \hbox (badness 10000) in paragraph at lines 48166--48169 []\T1/pcr/m/n/10 resA atomA nbondsA resB atomB nbondsB length newresA newresB [ atomI atomJ Overfull \hbox (10.25368pt too wide) in paragraph at lines 48373--48375 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 48386--48388 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 48402--48404 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48418--48420 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ [442] Underfull \hbox (badness 10000) in paragraph at lines 48468--48470 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 48481--48485 \T1/ptm/m/n/10 num-ber; residue [443] Underfull \hbox (badness 10000) in paragraph at lines 48619--48621 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 48622--48625 []|\T1/phv/m/n/10 num. Underfull \hbox (badness 10000) in paragraph at lines 48626--48629 []|\T1/phv/m/n/10 func. Underfull \hbox (badness 10000) in paragraph at lines 48633--48637 []|\T1/phv/m/n/10 use in Underfull \hbox (badness 10000) in paragraph at lines 48648--48650 []|\T1/phv/m/n/10 Topol-ogy file Overfull \hbox (35.51122pt too wide) in paragraph at lines 48720--48722 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Overfull \hbox (35.51122pt too wide) in paragraph at lines 48739--48741 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48748--48750 []|$\OML/cmm/m/it/10 b[]$ \T1/ptm/m/n/10 (nm); $\OML/cmm/m/it/10 D$ Overfull \hbox (35.51122pt too wide) in paragraph at lines 48758--48760 []|\T1/pcr/m/n/10 bonds[][][][][][][]\T1/ptm/m/n/10 ,[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48784--48786 []|\T1/ptm/m/n/10 har-monic Underfull \hbox (badness 10000) in paragraph at lines 48831--48833 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48854--48856 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 48873--48875 []|\T1/ptm/m/n/10 low, up$[]$,$[]$ Underfull \hbox (badness 10000) in paragraph at lines 48880--48882 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48903--48905 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 6157) in paragraph at lines 48915--48917 []|\T1/ptm/m/n/10 fudge QQ (); Underfull \hbox (badness 10000) in paragraph at lines 48915--48917 \OML/cmm/m/it/10 q[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 q[]$ \T1/ptm/m/n/10 (e) , Underfull \hbox (badness 10000) in paragraph at lines 48915--48917 \OML/cmm/m/it/10 V$[][][][][][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48919--48921 []|\T1/ptm/m/n/10 ex-tra LJ or Underfull \hbox (badness 10000) in paragraph at lines 48931--48933 []|$\OML/cmm/m/it/10 q[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 q[]$ \T1/ptm/m/n/10 (e); Underfull \hbox (badness 10000) in paragraph at lines 48931--48933 \OML/cmm/m/it/10 V$[][][][][][][]\T1/ptm/m/n/10 ; Overfull \hbox (5.75829pt too wide) in paragraph at lines 48938--48940 []|\T1/pcr/m/n/10 angles[][][][][][][]| Overfull \hbox (5.75829pt too wide) in paragraph at lines 48957--48959 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 48973--48975 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 10000) in paragraph at lines 48985--48987 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 48989--48991 []|\T1/ptm/m/n/10 cross bond- Underfull \hbox (badness 6542) in paragraph at lines 49001--49003 []|$\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 r[]$ Overfull \hbox (5.75829pt too wide) in paragraph at lines 49008--49010 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \T1/ptm/m/n/10 mol$[]$rad$[]$); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 r[]$ \T1/ptm/m/n/10 (nm); Underfull \hbox (badness 10000) in paragraph at lines 49017--49019 \OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Overfull \hbox (5.75829pt too wide) in paragraph at lines 49027--49029 []|\T1/pcr/m/n/10 angles[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49036--49038 []|$\OML/cmm/m/it/10 ^^R[]$ \T1/ptm/m/n/10 (deg); Underfull \hbox (badness 10000) in paragraph at lines 49052--49054 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 5592) in paragraph at lines 49071--49073 []|$\OML/cmm/m/it/10 a[]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 k[]$ \T1/ptm/m/n/10 ((kJ Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 []|\T1/ptm/m/n/10 Ryckaert- Underfull \hbox (badness 10000) in paragraph at lines 49134--49136 \T1/ptm/m/n/10 Bellemans Underfull \hbox (badness 7888) in paragraph at lines 49146--49148 []|$\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 C[]$\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 49153--49155 []|\T1/ptm/m/n/10 pe-ri-odic im- Underfull \hbox (badness 10000) in paragraph at lines 49172--49174 []|\T1/ptm/m/n/10 Fourier di-he- Underfull \hbox (badness 10000) in paragraph at lines 49203--49205 []|\T1/ptm/m/n/10 ta-ble num-ber Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 []|\T1/ptm/m/n/10 com-bined Underfull \hbox (badness 10000) in paragraph at lines 49245--49247 \T1/ptm/m/n/10 bending-torsion Underfull \hbox (badness 10000) in paragraph at lines 49270--49272 []|\T1/ptm/m/n/10 one or more Overfull \hbox (35.75829pt too wide) in paragraph at lines 49277--49279 []|\T1/pcr/m/n/10 constraints[][][][][][][]| Underfull \hbox (badness 10000) in paragraph at lines 49293--49295 []|\T1/ptm/m/n/10 con- Overfull \hbox (2.50536pt too wide) in paragraph at lines 49296--49298 []|\T1/pcr/m/n/10 constraints| Underfull \hbox (badness 10000) in paragraph at lines 49328--49330 []|\T1/ptm/m/n/10 1-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49331--49333 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49341--49343 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49344--49346 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49357--49359 []|\T1/ptm/m/n/10 2-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49360--49362 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49373--49375 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49376--49378 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49389--49391 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49392--49394 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49405--49407 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49408--49410 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49421--49423 []|\T1/ptm/m/n/10 3-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49424--49426 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49433--49435 []|$\OML/cmm/m/it/10 a$\T1/ptm/m/n/10 , $\OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 (); $\OML/cmm/m/it/10 c$ Underfull \hbox (badness 10000) in paragraph at lines 49437--49439 []|\T1/ptm/m/n/10 4-body vir-tual Underfull \hbox (badness 10000) in paragraph at lines 49440--49442 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49456--49458 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49465--49467 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49472--49474 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 []|\T1/ptm/m/n/10 one or more Underfull \hbox (badness 10000) in paragraph at lines 49481--49483 \T1/ptm/m/n/10 con-struct-ing Underfull \hbox (badness 10000) in paragraph at lines 49488--49490 []|\T1/pcr/m/n/10 virtual_- Underfull \hbox (badness 10000) in paragraph at lines 49503--49505 []|\T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49506--49508 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 []|\T1/ptm/m/n/10 flat-bottomed Underfull \hbox (badness 10000) in paragraph at lines 49522--49524 \T1/ptm/m/n/10 po-si-tion re- Underfull \hbox (badness 10000) in paragraph at lines 49525--49527 []|\T1/pcr/m/n/10 position_- Underfull \hbox (badness 10000) in paragraph at lines 49538--49540 []|\T1/ptm/m/n/10 dis-tance re- Underfull \hbox (badness 10000) in paragraph at lines 49541--49543 []|\T1/pcr/m/n/10 distance_- Underfull \hbox (badness 10000) in paragraph at lines 49550--49552 \T1/ptm/m/n/10 up$[]$,$[]$ (nm); Underfull \hbox (badness 10000) in paragraph at lines 49554--49556 []|\T1/ptm/m/n/10 di-he-dral re- Underfull \hbox (badness 10000) in paragraph at lines 49557--49559 []|\T1/pcr/m/n/10 dihedral_- Underfull \hbox (badness 10000) in paragraph at lines 49573--49575 []|\T1/ptm/m/n/10 ori-en-ta-tion Overfull \hbox (14.50536pt too wide) in paragraph at lines 49576--49578 []|\T1/pcr/m/n/10 orientation_- Underfull \hbox (badness 10000) in paragraph at lines 49585--49587 \T1/ptm/m/n/10 (U); weight Underfull \hbox (badness 10000) in paragraph at lines 49592--49594 []|\T1/pcr/m/n/10 angle_- Underfull \hbox (badness 10000) in paragraph at lines 49608--49610 []|\T1/ptm/m/n/10 an-gle re-straint Underfull \hbox (badness 10000) in paragraph at lines 49611--49613 []|\T1/pcr/m/n/10 angle_- Overfull \hbox (8.50536pt too wide) in paragraph at lines 49611--49613 \T1/pcr/m/n/10 restraints_- [444] [445] [446 pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { } pdfTeX warning (ext4): destination with the same identifier (name{sphinxfootnot emark.6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.49644 \item { }] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50190--50192 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) in paragraph at lines 50196--50198 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 A-state Underfull \hbox (badness 10000) detected at line 50199 \T1/phv/m/n/10 atom Underfull \hbox (badness 10000) detected at line 50199 []\T1/phv/m/n/10 B-state Underfull \hbox (badness 10000) in paragraph at lines 50222--50225 []\T1/phv/m/n/10 ex-pected Underfull \hbox (badness 10000) detected at line 50226 []\T1/phv/m/n/10 ex-pected [452] [453] [454] [455] [456] [457] [458] [459] [460 <./plotje.png>] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471 <./xvgr.png>] [472 <./lambda-values.pdf>] [473] [474 <./pull.pdf>] [475] [476 <./pullref.pdf>] [477 <./pulldirrel.pdf>] [478] [479] [480] [481 <./awh-traj.pdf> <./awh-invN.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-invN.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [482 <./awh-sampleweights.pdf> <./awh-pmfs.pdf pdfTeX warning: /usr/bin/pdflatex (file ./awh-pmfs.pdf): PDF inclusion: multipl e pdfs with page group included in a single page >] [483] [484] [485] [486] [487] [488 <./rotation.pdf>] [489 <./equipotential.pdf>] [490 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53629 \subsubsection{Radial Motion Potential} ] [491] [492 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.35 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53881 \end{equation} ] [493 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 6}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.53968 \end{equation} <./gaussians.pdf>] Overfull \hbox (1.42029pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 pivot| Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 slab- Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 min- Overfull \hbox (2.21065pt too wide) in paragraph at lines 54578--54578 []$[]$| Overfull \hbox (1.2207pt too wide) in paragraph at lines 54578--54578 []$[]$\T1/phv/m/n/10 /ps| Overfull \hbox (1.25058pt too wide) in paragraph at lines 54578--54578 []\T1/phv/m/n/10 nm$[]$| Underfull \hbox (badness 10000) in paragraph at lines 54578--54578 []\T1/ptm/m/n/10 par-al-lel mo- [494] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.37 0}) has been already used, duplicate ignored \relax l.54763 \begin{equation} \label{equation:reference-manual/special/enforced-ro... [495] [496] [497 <./field.pdf>] [498 <./compelsetup.pdf>] [499] [500] [501] [502 <./dumtypes.pdf> <./dumaro.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dumaro.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525 <./rdf.pdf>] [526 <./rdfO-O.pdf>] [527] [528] [529] [530 <./msdwater.pdf>] [531 <./dih-def.pdf> <./sgangle.pdf pdfTeX warning: /usr/bin/pdflatex (file ./sgangle.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [532 <./distm.pdf>] [533] [534] [535 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [536 <./phipsi.pdf>] [537 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [538] [539] [540 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58763 ...ecular shift (mol\sphinxhyphen{}shift)} ] [541] [542] [543 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 1}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59057 \end{equation} ] [544] [545 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... [546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59250 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61748--61751 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. [570] [571] [572] Overfull \vbox (1.4634pt too high) detected at line 62640 [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] [587] [588] Chapter 7. [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool [593] [594] [595] Chapter 8. [596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 68023--68029 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69147--69153 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [626] [627] [628 <./redmine-states.png>] [629] [630] [631] [632] [633] [634] [635] Overfull \vbox (2.30272pt too high) detected at line 70296 [636] [637] [638] Overfull \vbox (1.24654pt too high) detected at line 70499 [639] Underfull \vbox (badness 10000) detected at line 70499 Underfull \vbox (badness 10000) detected at line 70499 [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Chapter 9. [667] Chapter 10. Underfull \hbox (badness 10000) in paragraph at lines 73462--73466 \T1/ptm/m/n/10 (page 670[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73829--73833 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 7168) in paragraph at lines 75153--75158 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [685] [686] Underfull \hbox (badness 10000) in paragraph at lines 75311--75315 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 7722) in paragraph at lines 76624--76629 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Overfull \hbox (18.01631pt too wide) in paragraph at lines 87778--87781 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 87778--87781 [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] No file gromacs.ind. (./gromacs.aux) LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (837 pages, 13748976 bytes). Transcript written on gromacs.log. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target manual make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -j12 man -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 man make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 68 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/man.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-image-conversion.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 0%] Built target internal_rpc_xdr [ 0%] Built target scanner [ 5%] Built target sphinx-image-conversion /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 7%] Built target thread_mpi make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 8%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend [ 8%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/muparser /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 10%] Built target tng_io_zlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 11%] Built target muparser [ 11%] Built target lmfit_objlib [ 11%] Built target linearalgebra [ 13%] Built target options /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 13%] Built target energyanalysis [ 16%] Built target colvars_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 39%] Built target sphinx-input-rst make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target gmx_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target mdrun_objlib [ 41%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 41%] Built target taskassignment make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2025.0/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.0/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.0/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -j12 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 69 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/muparser /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-image-conversion.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 0%] Built target scanner [ 5%] Built target sphinx-image-conversion [ 7%] Built target tng_io_obj [ 7%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 7%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 8%] Built target tng_io_zlib [ 8%] Built target linearalgebra [ 10%] Built target thread_mpi [ 13%] Built target colvars_objlib /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend [ 14%] Built target muparser make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 14%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 15%] Built target options make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-source-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 15%] Built target energyanalysis make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake [ 21%] Built target gmx_objlib [ 40%] Built target sphinx-input-rst [ 42%] Built target doxygen-source-timestamp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version [ 42%] Built target mdrun_objlib [ 42%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build [ 42%] Built target doxygen-version /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target taskassignment /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake [ 43%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 15 of file 'Doxyfile-xml' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/pdf.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target manual /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2025.0/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.0/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp:64: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' at line 212 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 223 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp:168: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' at line 271 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 278 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' at line 286 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:257: warning: @copydetails or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copybrief or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copydetails or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copybrief or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copydetails or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:278: warning: @copydetails or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2025.0/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2025.0 -B /build/reproducible-path/gromacs-2025.0/build/documentation -o /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:35: SyntaxWarning: invalid escape sequence '\l' """Doxygen XML output parser. /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:343: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:350: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... Scanning source tree... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/testasserts.h:738: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:57: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:109: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:48: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:76: warning: Member CheckpointDataOperation (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (57), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (58), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (95), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:228: warning: unable to resolve reference to 'gmx_pme_reinit' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/gpu_timing.h:57: warning: Member PmeStage (enumeration) of file gpu_timing.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:250: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:274: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:229: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:235: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:240: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:258: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:266: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:181: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:70: warning: Member SimulationRunnerMdpSource (enumeration) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:71: warning: Member awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:113: warning: Member awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int shareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:170: warning: Member awhParamSerialized(AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int biasShareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:62: warning: Member plumedKernelAvailable() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp:402: warning: Member getNumberOfTestOpenMPThreads() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:417: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-lib /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run [ref.any] make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target webpage-sphinx The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'functions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'md_enums.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basicoptions.h' not generated, too many nodes (52), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'idef.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. warning: Included by graph for 'ifunc.h' not generated, too many nodes (91), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (371), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (252), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'enumerationhelpers.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (270), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (321), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (324), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes (230), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxy_gromacs_version.h:42: warning: Member COLVARPROXY_VERSION (macro definition) of file colvarproxy_gromacs_version.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:55: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:57: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:58: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:60: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:61: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:62: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:63: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:64: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:45: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:47: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:48: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:50: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:51: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:52: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:53: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:54: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp:278: warning: Member dd_bonded_cg_distance(const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb) (function) of file computemultibodycutoffs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:144: warning: Member dd_sendrecv2_rvec(const struct gmx_domdec_t gmx_unused *dd, int gmx_unused ddimind, rvec gmx_unused *buf_s_fw, int gmx_unused n_s_fw, rvec gmx_unused *buf_r_fw, int gmx_unused n_r_fw, rvec gmx_unused *buf_s_bw, int gmx_unused n_s_bw, rvec gmx_unused *buf_r_bw, int gmx_unused n_r_bw) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:230: warning: Member dd_bcast(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:240: warning: Member dd_scatter(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:259: warning: Member dd_gather(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:278: warning: Member dd_scatterv(const gmx_domdec_t gmx_unused *dd, gmx::ArrayRef< const int > gmx_unused scounts, gmx::ArrayRef< const int > gmx_unused disps, const T *sbuf, int rcount, T *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:321: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const int *sbuf, int rcount, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:328: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const gmx::RVec *sbuf, int rcount, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:336: warning: Member dd_gatherv(const gmx_domdec_t gmx_unused &dd, gmx::ArrayRef< const T > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > gmx_unused disps, gmx::ArrayRef< T > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:383: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const int > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< int > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:389: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const gmx::RVec > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< gmx::RVec > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:70: warning: Member supportedLibMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:73: warning: Member supportedThreadMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp:959: warning: Member dd_make_local_top(const gmx_domdec_t &dd, const gmx::DomdecZones &zones, int npbcdim, matrix box, rvec cellsize_min, const ivec npulse, t_forcerec *fr, ArrayRef< const RVec > coordinates, const gmx_mtop_t &mtop, gmx::ArrayRef< const int32_t > atomInfo, gmx_localtop_t *ltop) (function) of file localtopology.cpp is not documented. warning: Include graph for 'partition.cpp' not generated, too many nodes (61), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp:412: warning: Member dd_make_reverse_top(FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking) (function) of file reversetopology.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp:73: warning: Member cvec (typedef) of file ewald.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp:578: warning: Member initGrids(gmx::ArrayRef< PmeAndFftGrids > gridsSet, const gmx_pme_t &pme, const bool requestReproducibility, gmx::ArrayRef< std::vector< AlignedVector< real > > > gridsStorage) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp:1799: warning: Member parallel_3dfft_destroy(gmx_parallel_3dfft *pfft_setup) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:58: warning: Member hardware_destructive_interference_size (variable) of file pme_force_sender_gpu_impl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather_sycl.cpp:702: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather_sycl.cpp:706: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu.cpp:280: warning: Member pme_gpu_launch_gather(gmx_pme_t *pme, gmx_wallcycle gmx_unused *wcycle, const real lambdaQ, const bool computeVirial) (function) of file pme_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:90: warning: Member mode (typedef) of file pme_gpu_calculate_splines_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:102: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:107: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:112: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:116: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:61: warning: Member mode (typedef) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1404: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1409: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1414: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1418: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_hip_stubs.cpp:107: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *, bool) (function) of file pme_gpu_hip_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.cpp:1127: warning: Member pme_gpu_update_input_box(PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.cpp:2550: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.h:70: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.h:447: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:80: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:85: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:90: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:94: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:91: warning: Member INSTANTIATE_SPREAD_2( order, computeSplines, spreadCharges, numGrids, writeGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:94: warning: Member INSTANTIATE_SPREAD(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:100: warning: Member INSTANTIATE_GATHER_2(order, numGrids, readGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:103: warning: Member INSTANTIATE_GATHER(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:107: warning: Member INSTANTIATE_X(x, order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:113: warning: Member INSTANTIATE_SOLVE(subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:123: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:59: warning: Member c_pmeOrder (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:61: warning: Member c_wrapX (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:62: warning: Member c_wrapY (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:64: warning: Member c_stateA (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:65: warning: Member c_stateB (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp:484: warning: Member gmx_pme_send_resetcounters(const t_commrec gmx_unused *cr, int64_t gmx_unused step) (function) of file pme_pp.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:86: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:88: warning: Member PP_PME_RECVFTOGPU (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:90: warning: Member PP_PME_MDGPUGRAPH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve_sycl.cpp:54: warning: Member mode (typedef) of file pme_solve_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread_sycl.cpp:438: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread_sycl.cpp:444: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. warning: Included by graph for 'devicebuffer_datatype.h' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:70: warning: Member GMX_ALWAYS_INLINE (macro definition) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:96: warning: Member __attribute__((always_inline)) float gmxGpuFDim(const float one (function) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:96: warning: Member two (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:102: warning: Member value (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:120: warning: Member valueTwo (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:120: warning: Member valueThree (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:138: warning: Member d1 (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:138: warning: Member t (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:143: warning: Member offset (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp:82: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp:87: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_hip.cpp:91: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_hip.cpp:95: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_sycl.cpp:128: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *deviceContext) (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_sycl.cpp:137: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_hip.cpp:128: warning: Member determineIfDeviceHasLargeRegisterPool(std::string deviceArch) (function) of file device_management_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:68: warning: Member parseHardwareVersionNvidia(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:105: warning: Member getHardwareVersionNvidia(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:140: warning: Member parseHardwareVersionAmd(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:180: warning: Member getHardwareVersionAmd(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:214: warning: Member getHardwareVersionIntel(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:250: warning: Member getDeviceGpuAwareMpiStatus(const sycl::backend backend) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:548: warning: Member partitionDevices(const std::vector< sycl::device > &&devices) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:51: warning: Member IntelProductConfig (enumeration) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:611: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:622: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:138: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:113: warning: Member staggeredAtomicAddForce(sycl::global_ptr< Float3 > gm_f, Float3 f, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:134: warning: Member harmonic_gpu(const float kA, const float xA, const float x, sycl::private_ptr< float > V, sycl::private_ptr< float > F) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:152: warning: Member bonds_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:260: warning: Member bond_angle_gpu(const sycl::float4 xi, const sycl::float4 xj, const sycl::float4 xk, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< float > costh, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:279: warning: Member angles_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:347: warning: Member urey_bradley_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:460: warning: Member dih_angle_gpu(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< int > t3) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:489: warning: Member dih_angle_gpu_sincos(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< float > cosval) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:529: warning: Member dopdihs_gpu(const float cpA, const float phiA, const int mult, const float phi, sycl::private_ptr< float > v, sycl::private_ptr< float > f) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:543: warning: Member do_dih_fup_gpu(const int i, const int j, const int k, const int l, const float ddphi, const Float3 r_ij, const Float3 r_kj, const Float3 r_kl, const Float3 m, const Float3 n, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const sycl::global_ptr< const Float4 > gm_xq, const int t1, const int t2, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:603: warning: Member pdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:649: warning: Member rbdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:761: warning: Member idihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:814: warning: Member pairs_gpu(const int i, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_iparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const float scale_factor, sycl::private_ptr< float > vtotVdw_loc, sycl::private_ptr< float > vtotElec_loc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp:173: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:107: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:109: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:111: warning: Member pvEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:113: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:115: warning: Member virialEnergyFieldNames (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:119: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:132: warning: Member haveFepLambdaMoves(const t_inputrec &inputrec) (function) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.h:63: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.h:61: warning: Member GPU_LEAPFROG_SUPPORTED (macro definition) of file leapfrogtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.h:61: warning: Member GPU_SETTLE_SUPPORTED (macro definition) of file settletestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:69: warning: Member sc_haveGpuConstraintSupport (variable) of file update_constrain_gpu_impl.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'mimic.cpp' not generated, too many nodes (64), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'minimize.cpp' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. warning: Include graph for 'rerun.cpp' not generated, too many nodes (66), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. warning: Include graph for 'runner.cpp' not generated, too many nodes (112), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. warning: Include graph for 'tpi.cpp' not generated, too many nodes (50), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:186: warning: Member gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:195: warning: Member gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:204: warning: Member gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:213: warning: Member gmx_sumli_sim(int gmx_unused nr, int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:391: warning: Member multisim_int_all_are_equal(const gmx_multisim_t *ms, int64_t value) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_simd.h:137: warning: Member GMX_HAVE_NBNXM_SIMD_4XM (macro definition) of file nbnxm_simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_gpu_buffer_ops_internal_sycl.cpp:50: warning: Member mode (typedef) of file nbnxm_gpu_buffer_ops_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:51: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_8 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:52: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_32 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:53: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_64 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_pruneonly.cpp:55: warning: Member mode (typedef) of file nbnxm_sycl_kernel_pruneonly.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp:1433: warning: Member putAtomsInBoxTemplated(PbcType pbcType, const matrix box, const matrix boxDeformation, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v) (function) of file pbc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp:56: warning: Member set_pbc_simd(const t_pbc gmx_unused *pbc, real gmx_unused *pbc_simd) (function) of file pbc_simd.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2029: warning: found documented return type for analyze_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1844: warning: found documented return type for evaluate_boolean_static_part that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1766: warning: found documented return type for init_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1713: warning: found documented return type for process_const that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp:905: warning: found documented return type for parse_values_enum that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp:364: warning: found documented return type for convert_real_int that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp:126: warning: found documented return type for init_compare that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp:102: warning: found documented return type for init_common that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp:120: warning: found documented return type for init_frame_common that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:255: warning: found documented return type for init_insolidangle that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:353: warning: found documented return type for init_kweval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:113: warning: found documented return type for init_kwreal that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:365: warning: found documented return type for init_output_kweval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp:77: warning: found documented return type for init_merge that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp:90: warning: found documented return type for init_permute that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:100: warning: found documented return type for init_cog that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:110: warning: found documented return type for init_com that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:87: warning: found documented return type for init_kwpos that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:120: warning: found documented return type for init_output_pos that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp:121: warning: found documented return type for init_same that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp:90: warning: found documented return type for check_molecules that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp:160: warning: found documented return type for check_pdbinfo that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:123: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:124: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:132: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:142: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:143: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:144: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:145: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:149: warning: Member c_maxAutoTmpiRanksPerGpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/instrumentation.h:216: warning: Member traceRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/instrumentation.h:217: warning: Member traceSubRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:198: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:130: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:143: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:156: warning: Member checkParticle(TestReferenceChecker *checker, const SimulationParticle &particle) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:201: warning: Member testParticleMassOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:202: warning: Member testParticleMassTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:203: warning: Member testParticleChargeOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:204: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:205: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:206: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp:332: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (110), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxmpi.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. warning: Included by graph for 'logger.h' not generated, too many nodes (51), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. warning: Included by graph for 'gmxpre.h' not generated, too many nodes (792), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (98), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (113), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes (200), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testfilemanager.h' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selection.h:36: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.h:115: warning: Member GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(bonded_threading_t) (function) of struct bonded_threading_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:121: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:122: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:137: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:138: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:139: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:140: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:141: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:106: warning: Member gmx_pme_pp(MPI_Comm simulationCommunicator, std::vector< PpRanks > &&ppRanks) (function) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:113: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:114: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:115: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:116: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:117: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:124: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:158: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:159: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:160: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:161: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:162: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:168: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:169: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:170: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:171: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:263: warning: Member useNvshmem (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:265: warning: Member nvshmemParams (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:175: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl) (function) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:114: warning: Member splineKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member spreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member spreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member splineAndSpreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:119: warning: Member splineAndSpreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:120: warning: Member splineAndSpreadKernelWriteSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:121: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:122: warning: Member splineKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:123: warning: Member splineKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:124: warning: Member spreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:125: warning: Member spreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:126: warning: Member splineAndSpreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:127: warning: Member splineAndSpreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:128: warning: Member splineAndSpreadKernelWriteSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:142: warning: Member gatherKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:143: warning: Member gatherKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:144: warning: Member gatherKernelReadSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member gatherKernelReadSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member gatherKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member gatherKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member gatherKernelReadSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:149: warning: Member gatherKernelReadSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:159: warning: Member solveYZXKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:160: warning: Member solveXYZKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:161: warning: Member solveYZXEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:162: warning: Member solveXYZEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:163: warning: Member solveYZXKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:164: warning: Member solveXYZKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:165: warning: Member solveYZXEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:166: warning: Member solveXYZEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:168: warning: Member nvshmemSignalKern (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:88: warning: Member t_forcetable(TableInteraction interaction, TableFormat format) (function) of struct t_forcetable is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnTpr (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnCoordSel (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:229: warning: Member bPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member min (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member max (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member dz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:243: warning: Member Temperature (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:259: warning: Member bBoundsOnly (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:270: warning: Member bTauIntGiven (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:281: warning: Member bHistEq (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:307: warning: Member bsMethod (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:310: warning: Member tauBootStrap (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:314: warning: Member histBootStrapBlockLength (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:320: warning: Member bs_verbose (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:326: warning: Member bTab (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabX (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabY (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabDz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:328: warning: Member tabNbins (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:99: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:100: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:101: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:103: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp:272: warning: Member operator()(const std::array< std::byte, N > &a) const noexcept (function) of struct anonymous_namespace{device_management_common.cpp}::HashAnArray is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp:946: warning: Member mdModulesNotifiers (variable) of class anonymous_namespace{minimize.cpp}::EnergyEvaluator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:147: warning: Member AspartateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:169: warning: Member GlutamateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:191: warning: Member GlutamineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:213: warning: Member LysineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:234: warning: Member ArginineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1300: warning: Member ChainSeparationType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1562: warning: Member VSitesType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1573: warning: Member WaterType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1589: warning: Member MergeType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:127: warning: Member res2bb_notermini(const std::string &name, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:139: warning: Member enumValueToLongString(HistidineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:154: warning: Member enumValueToString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:161: warning: Member enumValueToLongString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:176: warning: Member enumValueToString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:183: warning: Member enumValueToLongString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:198: warning: Member enumValueToString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:205: warning: Member enumValueToLongString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:220: warning: Member enumValueToString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:226: warning: Member enumValueToLongString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:241: warning: Member enumValueToString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:248: warning: Member enumValueToLongString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:257: warning: Member select_res(int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:279: warning: Member get_asptp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:284: warning: Member get_glutp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:289: warning: Member get_glntp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:294: warning: Member get_lystp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:299: warning: Member get_argtp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:304: warning: Member get_histp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:309: warning: Member read_rtprename(const char *fname, FILE *fp, std::vector< RtpRename > *rtprename) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:367: warning: Member search_resrename(gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:413: warning: Member rename_resrtp(t_atoms *pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab *symtab, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:471: warning: Member pdbres_to_gmxrtp(t_atoms *pdba) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:484: warning: Member rename_pdbres(t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:579: warning: Member check_occupancy(t_atoms *atoms, const char *filename, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:642: warning: Member write_posres(const char *fn, t_atoms *pdba, real fc) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:671: warning: Member read_pdball(const char *inf, bool bOutput, const char *outf, char **title, t_atoms *atoms, rvec **x, PbcType *pbcType, matrix box, bool bRemoveH, t_symtab *symtab, const ResidueTypeMap &residueTypeMap, const char *watres, AtomProperties *aps, bool bVerbose) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:745: warning: Member process_chain(const gmx::MDLogger &logger, t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:835: warning: Member pdbicomp(const t_pdbindex &a, const t_pdbindex &b) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:853: warning: Member sort_pdbatoms(gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:939: warning: Member remove_duplicate_atoms(t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1011: warning: Member checkResidueTypeSanity(t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1085: warning: Member find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1320: warning: Member modify_chain_numbers(t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1444: warning: Member checkChainCyclicity(t_atoms *pdba, rvec *pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1309: warning: Member c_chainSeparationTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1312: warning: Member c_chainSeparationTypeNotificationMessages (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1569: warning: Member c_vsitesTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1585: warning: Member c_waterTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1596: warning: Member c_mergeTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp:95: warning: Member c_currentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp:200: warning: Member c_dfHistoryCurrentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:73: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:74: warning: Member flag (variable) of struct gmx::CacheLineAlignedFlag is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:446: warning: Member mtop (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:447: warning: Member effectiveAtomDensity (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:448: warning: Member inputrec (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:449: warning: Member pressureTolerance (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:450: warning: Member listSetup (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:451: warning: Member useGpuList (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:452: warning: Member mtsFactor (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp:392: warning: Member getElementPointerImpl(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp:426: warning: Member getElementPointerImpl(LegacySimulatorData *simulator, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.h:86: warning: found documented return type for gmx::CoordState::sampleUmbrellaGridpoint that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:104: warning: Member DomdecZones(ArrayRef< const int > ddDims) (function) of class gmx::DomdecZones is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:134: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:250: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:274: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:229: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:235: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:240: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:258: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:266: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:181: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:236: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionstorage.h:74: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::FileNameOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:162: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:80: warning: Member x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:82: warning: Member x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:84: warning: Member bb_x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:86: warning: Member bb_x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:180: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:181: warning: Member pmeStream_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:105: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:106: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:107: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:108: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:109: warning: Member deviceStream_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:111: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:106: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:107: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:108: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:109: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:110: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:111: warning: Member context_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:112: warning: Member device_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:113: warning: Member commandQueue_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:115: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_rocfft.cpp:240: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:124: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:125: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:126: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:127: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:128: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:129: warning: Member queue_device_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:131: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction.h:125: warning: Member registerForcesReadyNvshmemFlags(DeviceBuffer< uint64_t > syncObj) (function) of class gmx::GpuForceReduction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.h:137: warning: Member setNonLocalGrid(const int gridIndex, const int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::GridSet is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:115: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:95: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:133: warning: Member value (variable) of struct gmx::IsSerializableType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:226: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:227: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:228: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:229: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:230: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.h:146: warning: Member Graph (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.h:147: warning: Member GraphInstance (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:149: warning: Member kernel_noener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:150: warning: Member kernel_ener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:151: warning: Member kernel_noener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:152: warning: Member kernel_ener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:162: warning: Member kernel_memset_f (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:163: warning: Member kernel_memset_f2 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:164: warning: Member kernel_memset_f3 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.h:184: warning: Member nbnxn_atomdata_t(PinningPolicy pinningPolicy) (function) of struct gmx::nbnxn_atomdata_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.h:224: warning: Member SimdMasks(NbnxmKernelType kernelType) (function) of struct gmx::nbnxn_atomdata_t::SimdMasks is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider.h:65: warning: Member NNPotForceProvider(const NNPotParameters &, const MDLogger *logger) (function) of class gmx::NNPotForceProvider is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.h:108: warning: Member modelNeedsInput(const std::string &input) const (function) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.h:103: warning: Member numAtoms_ (variable) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:138: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider.h:69: warning: Member QMMMForceProvider(const QMMMParameters ¶meters, const LocalAtomSet &localQMAtomSet, const LocalAtomSet &localMMAtomSet, PbcType pbcType, const MDLogger &logger) (function) of class gmx::QMMMForceProvider is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtypes.h:142: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters) (function) of struct gmx::QMMMParameters is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h:287: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:63: warning: Member ScalingMatrix(const Matrix3x3 &m) (function) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member xx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zz (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member yx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zy (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:415: warning: found documented return type for gmx::SelectionEvaluator::evaluate that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:139: warning: Member SimulationInputHandle(const SimulationInputHandle &source) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:140: warning: Member SimulationInputHandle(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:142: warning: Member operator=(const SimulationInputHandle &rhs) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:143: warning: Member operator=(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:191: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::StringOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:177: warning: Member TestParticleInsertion(const t_inputrec &inputRec, const gmx_mtop_t &topGlobal, const gmx_localtop_t &top, const t_mdatoms &mdatoms, const MDModulesNotifiers &mdModulesNotifiers, t_forcerec *forceRec, gmx_enerdata_t *enerd, const Range< int > &testAtomsRange, ArrayRef< const RVec > xMoleculeToInsert, real beta, real rfExclusionEnergy, real referenceVolume, int numTasks, int taskIndex) (function) of class gmx::TestParticleInsertion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.h:120: warning: Member processMask() (function) of class gmx::ThreadForceBuffer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:131: warning: Member update_coords(const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, t_state *state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata *fcdata, const gmx_ekindata_t *ekind, const Matrix3x3 &parrinelloRahmanM, int UpdatePart, const t_commrec *cr, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:147: warning: Member finish_update(const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, gmx::ArrayRef< const unsigned short > cFREEZE, t_state *state, gmx_wallcycle *wcycle, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:155: warning: Member update_sd_second_half(const t_inputrec &inputRecord, int64_t step, real *dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state *state, const t_commrec *cr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx::Constraints *constr, bool do_log, bool do_ene) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:169: warning: Member update_for_constraint_virial(const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:178: warning: Member update_temperature_constants(const t_inputrec &inputRecord, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:180: warning: Member getAndersenRandomizeGroup() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:182: warning: Member getBoltzmanFactor() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:184: warning: Member xp() (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:186: warning: Member deform() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:135: warning: Member HbondStorageFrame(int frnr, std::vector< HBond > data) (function) of struct gmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrame is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:294: warning: Member MsdCoordinateManager(const int numAtoms, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeIndexMapping) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:124: warning: Member MsdColumnProxy(std::vector< double > *column) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:126: warning: Member push_back(double value) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:380: warning: Member MsdGroupData(const Selection &inputSel, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeAtomMapping) (function) of struct gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp:242: warning: Member filterBondComm (variable) of struct gmx::anonymous_namespace{domainpaircomm.cpp}::DistanceCalculationInfo is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp:160: warning: Member dispatchFreeEnergyKernel(gmx::ArrayRef< const std::unique_ptr< t_nblist > > nbl_fep, const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, const bool clearForcesAndEnergies, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForceBuffer, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForeignEnergyBuffer, gmx_grppairener_t *foreignGroupPairEnergies, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb) (function) of namespace gmx::anonymous_namespace{freeenergydispatch.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:110: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t gmx_unused *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:112: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:120: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:122: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:136: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:138: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:49: warning: Member c_nBoxZ (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:50: warning: Member c_nBoxY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:51: warning: Member c_nBoxX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:52: warning: Member c_numIvecs (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options_impl.h:200: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl) (function) of class gmx::internal::OptionSectionImpl is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.h:74: warning: Member AwhTestParameters(ISerializer *serializer) (function) of struct gmx::test::AwhTestParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::GyrateInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::HbondInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp:276: warning: Member operator()(const testing::TestParamInfo< ParamType > ¶meter) const (function) of struct gmx::test::PrintReplicaExchangeParametersToString is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:162: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:163: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:164: warning: Member mdpFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:165: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:166: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:167: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:168: warning: Member cptOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:169: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:170: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:171: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:172: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:173: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:174: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:175: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:176: warning: Member dhdlFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:177: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:178: warning: Member maxwarn_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:73: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:74: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:75: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:86: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:87: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:104: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:106: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:112: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:113: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:147: warning: Member grid_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:148: warning: Member gridIndexToDataIndex_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:149: warning: Member data_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:150: warning: Member numColumns_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:151: warning: Member numRows_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:152: warning: Member filename_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:361: warning: Member WriteFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:362: warning: Member TestFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:371: warning: Member addTestValues() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:389: warning: Member test() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:365: warning: Member writeFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:367: warning: Member testFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:437: warning: Member addTestValueFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:453: warning: Member testingTypes_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:467: warning: Member fileManager_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:468: warning: Member filename_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:77: warning: Member value (variable) of struct gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:184: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:190: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:196: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:202: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:208: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:118: warning: Member begin() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:119: warning: Member end() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:109: warning: Member Iterator(const T *ptr) (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:110: warning: Member operator++() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:111: warning: Member operator!=(const Iterator &other) const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:112: warning: Member operator*() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp:266: warning: Member ViewMatchesCString(const std::string_view view) (function) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp:265: warning: Member view_ (variable) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:93: warning: Member currentState (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:94: warning: Member perLambdaInformation (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:95: warning: Member finalPos (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:82: warning: Member index (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member count (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member G (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member dG (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp:102: warning: Member setGroup(const int(&atoms)[count]) (function) of class gmx::test::anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:280: warning: Member KernelInputParameters(TupleT t) (function) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp:62: warning: Member setupMTop(gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds) (function) of namespace gmx::test::anonymous_namespace{massrepartitioning.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:260: warning: Member runTest(const HardwareTopology &hwTop) (function) of class gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:361: warning: Member getNbList() (function) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:344: warning: Member idef (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:347: warning: Member chargeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:348: warning: Member chargeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:349: warning: Member typeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:350: warning: Member typeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:354: warning: Member iAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:355: warning: Member jAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:356: warning: Member shift (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:357: warning: Member gid (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:358: warning: Member exclFep (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:111: warning: Member OutputQuantities(int energyGroup) (function) of struct gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:149: warning: Member sc_boxShapeNames (variable) of namespace gmx::test::anonymous_namespace{parrinellorahman.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:180: warning: Member operator()(const Matrix3x3 &matrix) const (function) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:179: warning: Member prefix (variable) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::ScatteringInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:49: warning: Member Options (enumeration) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:58: warning: Member testEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:64: warning: Member testBoolEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:70: warning: Member testBoolDoubleOrNot(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp:79: warning: Member delayInMilliseconds (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp:80: warning: Member wcycle (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. /build/reproducible-path/gromacs-2025.0/docs/doxygen/directories.cpp:96: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E remove -f /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/manual-2025.0-Debian_2025.0_2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/gromacs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/manual-2025.0-Debian_2025.0_2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E echo "Webpage output: file:///build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/index.html" Webpage output: file:///build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/index.html make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' touch build-manual dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -j12 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target scanner [ 0%] Built target internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target lmfit_objlib [ 2%] Built target tng_io_obj [ 2%] Built target release-version-info [ 6%] Built target options [ 6%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 6%] Built target mdrun_objlib [ 6%] Built target energyanalysis [ 10%] Built target colvars_objlib [ 12%] Built target gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 14%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 14%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target gmx [ 96%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" [ 98%] Built target argon-forces-integration [ 98%] Built target methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target gmxapi_extension_ensemblepotential [ 98%] Built target _gmxapi [ 98%] Built target gmxapi_extension_test /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target gmxapi_extension make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/phbres.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_mpi.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs_mpi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs_mpi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_mpi.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -j12 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target scanner [ 0%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build [ 0%] Built target thread_mpi [ 0%] Built target internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target lmfit_objlib [ 0%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" [ 0%] Built target energyanalysis [ 0%] Built target options [ 0%] Built target mdrun_objlib [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target gmx_objlib [ 4%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 4%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 4%] Built target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 95%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 97%] Built target gmxapi [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target argon-forces-integration [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_mpi_d.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs-hints_mpi_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi_d -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -j12 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 0%] Built target internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target lmfit_objlib [ 2%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build [ 4%] Built target energyanalysis [ 4%] Built target tng_io_obj [ 6%] Built target options make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 6%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 6%] Built target mdrun_objlib [ 10%] Built target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 10%] Built target gmx_objlib [ 14%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 16%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 16%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/share/template /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/share/template /build/reproducible-path/gromacs-2025.0/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 96%] Built target gmx [ 98%] Built target gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target template [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/README -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/template.cpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/Makefile.pkg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/topology_enums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectory -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/trxio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/pbcutil -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/restraint -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-hints.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -j12 -C build/basic-dp install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target internal_rpc_xdr make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target scanner [ 0%] Built target energyanalysis /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 0%] Built target lmfit_objlib [ 2%] Built target options [ 2%] Built target mdrun_objlib [ 2%] Built target linearalgebra [ 6%] Built target thread_mpi /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 6%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 8%] Built target tng_io_obj [ 8%] Built target gmx_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 14%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 14%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target gmx [100%] Built target gmxapi [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs-hints_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* perl -lne 'print' /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash \ /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-*.bash > \ /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-concat mv /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux mv /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_bash-completion -a dh_lintian -a dh_link -a dh_testdir -i dh_testroot -i dh_installdirs -i dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installman -i find /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc", found 24745 files. Now have 24745 files in total. Removed 0 files due to nonunique device and inode. Total size is 413576316 bytes or 394 MiB Removed 8199 files due to unique sizes from list. 16546 files left. Now eliminating candidates based on first bytes: removed 3534 files from list. 13012 files left. Now eliminating candidates based on last bytes: removed 1798 files from list. 11214 files left. Now eliminating candidates based on sha1 checksum: removed 3651 files from list. 7563 files left. It seems like you have 7563 files that are not unique Totally, 25 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 4403 links. symlinks -r -s -c /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/ absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2024/major/api.rst.txt changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> ../../2024/major/api.rst.txt absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> ../html-full/jquery.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> ../html-lib/dir_000021_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000089_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000002.xhtml -> ../html-lib/dir_000089_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams.xhtml -> ../html-full/uniont__iparams.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000066_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000067_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000066_000002.xhtml -> ../html-lib/dir_000067_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000153_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000154_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000153_000002.xhtml -> ../html-lib/dir_000154_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000134_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000002.xhtml -> ../html-lib/dir_000134_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> ../html-full/outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> ../html-full/doxygen.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/state_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> ../html-full/state_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> ../html-full/uniont__iparams-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> ../html-lib/dir_000009_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000019_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000019_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000019_000002.xhtml -> ../html-lib/dir_000019_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000073_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000002.xhtml -> ../html-lib/dir_000073_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000086_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> ../html-lib/dir_000086_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hostallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> ../html-full/hostallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> ../html-lib/classgmx_1_1TextLineWrapper.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gammadistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> ../html-full/gammadistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputselector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> ../html-full/outputselector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000152_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> ../html-lib/dir_000152_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000074_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000075_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000074_000002.xhtml -> ../html-lib/dir_000075_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000007.xhtml -> ../html-lib/dir_000023_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000091_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000092_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000091_000002.xhtml -> ../html-lib/dir_000092_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> ../html-full/classgmx_1_1NormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommBackward.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommBackward.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommBackward.xhtml -> ../html-lib/classgmx_1_1DomainCommBackward.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bench__system_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bench__system_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bench__system_8h__incl.svg -> ../html-full/bench__system_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/repeatingsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> ../html-full/repeatingsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/basicoptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__incl.svg -> ../html-full/basicoptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h__incl.svg -> ../html-full/selectionoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectioncollection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h__incl.svg -> ../html-full/selectioncollection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinerunner_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__incl.svg -> ../html-full/cmdlinerunner_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000145_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000002.xhtml -> ../html-lib/dir_000145_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ListOfLists.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists.xhtml -> ../html-full/classgmx_1_1ListOfLists.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/average_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__incl.svg -> ../html-full/average_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/histogram_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.svg -> ../html-full/histogram_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_12.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_17.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_12.svg -> ../html-full/msc_inline_mscgraph_17.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_11.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_6.svg -> ../html-full/msc_inline_mscgraph_11.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000002.xhtml -> ../html-lib/dir_000146_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structCheckpointHeaderContents.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structCheckpointHeaderContents.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structCheckpointHeaderContents.xhtml -> ../html-full/structCheckpointHeaderContents.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000006_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000002.xhtml -> ../html-lib/dir_000006_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/coordinatefile_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/coordinatefile_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/coordinatefile_8h__incl.svg -> ../html-full/coordinatefile_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lifetime_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.svg -> ../html-full/lifetime_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/threefry_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h__incl.svg -> ../html-full/threefry_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg -> ../html-full/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/paddedvector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/paddedvector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/paddedvector_8h__incl.svg -> ../html-full/paddedvector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1EnergyFunctionProperties.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyFunctionProperties.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1EnergyFunctionProperties.xhtml -> ../html-lib/structgmx_1_1EnergyFunctionProperties.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1H5md.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1H5md.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1H5md.xhtml -> ../html-full/classgmx_1_1H5md.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataValue.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue.xhtml -> ../html-full/classgmx_1_1AnalysisDataValue.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000093_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000002.xhtml -> ../html-lib/dir_000093_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000139_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000140_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000139_000002.xhtml -> ../html-lib/dir_000140_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000123_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000124_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000123_000002.xhtml -> ../html-lib/dir_000124_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/listoflists_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/listoflists_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/listoflists_8h__incl.svg -> ../html-full/listoflists_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior.xhtml -> ../html-lib/classgmx_1_1SelectionOptionBehavior.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_14.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_21.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_14.svg -> ../html-lib/inherit_graph_21.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PaddedVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PaddedVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PaddedVector-members.xhtml -> ../html-full/classgmx_1_1PaddedVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000129_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000002.xhtml -> ../html-lib/dir_000129_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPairSearch.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPairSearch.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPairSearch.xhtml -> ../html-lib/classgmx_1_1AnalysisNeighborhoodPairSearch.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arraydata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__incl.svg -> ../html-full/arraydata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h__incl.svg -> ../html-full/selection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000150_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000151_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000150_000002.xhtml -> ../html-lib/dir_000151_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000012_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000012_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000012_000002.xhtml -> ../html-lib/dir_000012_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000002.xhtml -> ../html-lib/dir_000024_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000132_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000133_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000132_000002.xhtml -> ../html-lib/dir_000133_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadaptercontainer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadaptercontainer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadaptercontainer_8h__incl.svg -> ../html-full/outputadaptercontainer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FixedCapacityVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FixedCapacityVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FixedCapacityVector-members.xhtml -> ../html-full/classgmx_1_1FixedCapacityVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1INNPotModel.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel.xhtml -> ../html-lib/classgmx_1_1INNPotModel.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/exponentialdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h__incl.svg -> ../html-full/exponentialdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/normaldistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h__incl.svg -> ../html-full/normaldistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DataFileFinder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileFinder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DataFileFinder.xhtml -> ../html-lib/classgmx_1_1DataFileFinder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000002.xhtml -> ../html-lib/dir_000120_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000110_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000110_000002.xhtml -> ../html-full/dir_000111_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/utility_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/utility_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/utility_8h__incl.svg -> ../html-full/utility_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000125_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000126_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000125_000002.xhtml -> ../html-lib/dir_000126_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineParser.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineParser.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineParser.xhtml -> ../html-lib/classgmx_1_1CommandLineParser.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameHeader.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameHeader.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameHeader.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameHeader.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionList.xhtml -> ../html-full/structInteractionList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.svg -> ../html-full/doxygen.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dataframe_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dataframe_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dataframe_8h__incl.svg -> ../html-full/dataframe_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector.xhtml -> ../html-lib/classgmx_1_1OutputSelector.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms.xhtml -> ../html-lib/classgmx_1_1SetAtoms.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/histogram_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h.xhtml -> ../html-lib/histogram_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionsection_8h__incl.svg -> ../html-full/optionsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities.xhtml -> ../html-lib/classgmx_1_1SetVelocities.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision.xhtml -> ../html-lib/classgmx_1_1SetPrecision.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces.xhtml -> ../html-lib/classgmx_1_1SetForces.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep.xhtml -> ../html-lib/classgmx_1_1SetTimeStep.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nbsearch_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h__incl.svg -> ../html-full/nbsearch_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime.xhtml -> ../html-lib/classgmx_1_1SetStartTime.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000137_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000138_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000137_000002.xhtml -> ../html-lib/dir_000138_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tabulatednormaldistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h__incl.svg -> ../html-full/tabulatednormaldistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BenchmarkSystem.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem.xhtml -> ../html-lib/structgmx_1_1BenchmarkSystem.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BasicVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BasicVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BasicVector-members.xhtml -> ../html-full/classgmx_1_1BasicVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter.xhtml -> ../html-full/classgmx_1_1IOutputAdapter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniformrealdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h__incl.svg -> ../html-full/uniformrealdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1GammaDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1NormalDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000129_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000130_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000129_000002.xhtml -> ../html-lib/dir_000130_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FlagsTemplate.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FlagsTemplate.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FlagsTemplate.xhtml -> ../html-full/classgmx_1_1FlagsTemplate.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classWarningHandler.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classWarningHandler.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classWarningHandler.xhtml -> ../html-full/classWarningHandler.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_11.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_16.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_11.svg -> ../html-full/msc_inline_mscgraph_16.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.svg -> ../html-full/selectionoptionmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoptionmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenameoptionmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoptionmanager_8h__incl.svg -> ../html-full/filenameoptionmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__indexmap__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__indexmap__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__indexmap__t.xhtml -> ../html-lib/structgmx__ana__indexmap__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h__incl.svg -> ../html-full/abstractsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setatoms_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h__incl.svg -> ../html-full/setatoms_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__kernel__utils_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__kernel__utils_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__kernel__utils_8h.xhtml -> ../html-lib/hip__kernel__utils_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arrayrefwithpadding_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arrayrefwithpadding_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arrayrefwithpadding_8h__incl.svg -> ../html-full/arrayrefwithpadding_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000131_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000132_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000131_000002.xhtml -> ../html-lib/dir_000132_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotSettings.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPlotSettings.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ArrayRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ArrayRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ArrayRef-members.xhtml -> ../html-full/classgmx_1_1ArrayRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommForward.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommForward.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommForward.xhtml -> ../html-lib/classgmx_1_1DomainCommForward.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisHistogramSettings.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisHistogramSettings.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisHistogramSettings.xhtml -> ../html-lib/classgmx_1_1AnalysisHistogramSettings.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions.xhtml -> ../html-full/classInteractionDefinitions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/futil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/futil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/futil_8h__incl.svg -> ../html-full/futil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox.xhtml -> ../html-lib/classgmx_1_1SetBox.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomsetdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h__incl.svg -> ../html-lib/localatomsetdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__sycl__kernel__utils_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__sycl__kernel__utils_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__sycl__kernel__utils_8h.xhtml -> ../html-lib/hip__sycl__kernel__utils_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxnPairlistCpu.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu.xhtml -> ../html-lib/structgmx_1_1NbnxnPairlistCpu.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IAnalysisDataModule__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule__inherit__graph.svg -> ../html-lib/classgmx_1_1IAnalysisDataModule__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__oriresdata-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__oriresdata-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__oriresdata-members.xhtml -> ../html-full/structt__oriresdata-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef.xhtml -> ../html-full/structt__idef.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000078_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000079_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000078_000002.xhtml -> ../html-lib/dir_000079_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__random.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__random.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__random.xhtml -> ../html-lib/group__module__random.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPdbAtomEntry.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry.xhtml -> ../html-full/classPdbAtomEntry.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/requirements_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/requirements_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/requirements_8h__incl.svg -> ../html-full/requirements_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformintdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniformintdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformintdistribution_8h__incl.svg -> ../html-full/uniformintdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml -> ../html-lib/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classt__state-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__state-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classt__state-members.xhtml -> ../html-full/classt__state-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_10.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_15.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_10.svg -> ../html-full/msc_inline_mscgraph_15.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainPairComm.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainPairComm.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainPairComm.xhtml -> ../html-lib/classgmx_1_1DomainPairComm.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000083_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000084_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000083_000002.xhtml -> ../html-lib/dir_000084_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPmeSolve.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPmeSolve.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPmeSolve.xhtml -> ../html-full/classPmeSolve.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Range_1_1iterator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator.xhtml -> ../html-full/structgmx_1_1Range_1_1iterator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000077_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000078_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000077_000002.xhtml -> ../html-lib/dir_000078_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisData__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisData__inherit__graph.svg -> ../html-lib/classgmx_1_1AbstractAnalysisData__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000137_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000002.xhtml -> ../html-lib/dir_000137_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exceptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/exceptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exceptions_8h__incl.svg -> ../html-full/exceptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classSimulationParticle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classSimulationParticle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classSimulationParticle-members.xhtml -> ../html-full/classSimulationParticle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg -> ../html-full/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structCheckpointHeaderContents-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structCheckpointHeaderContents-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structCheckpointHeaderContents-members.xhtml -> ../html-full/structCheckpointHeaderContents-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fatalerror_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fatalerror_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fatalerror_8h__incl.svg -> ../html-full/fatalerror_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_95717a81c2d2f4488fb73b9bd8027da2.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_95717a81c2d2f4488fb73b9bd8027da2.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_95717a81c2d2f4488fb73b9bd8027da2.xhtml -> ../html-lib/dir_95717a81c2d2f4488fb73b9bd8027da2.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_5.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_10.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_5.svg -> ../html-full/msc_inline_mscgraph_10.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SelectionTopologyProperties.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties.xhtml -> ../html-full/structgmx_1_1SelectionTopologyProperties.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_8.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_3.svg -> ../html-full/msc_inline_mscgraph_8.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OutputRequirements.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements.xhtml -> ../html-full/structgmx_1_1OutputRequirements.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/datafilefinder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/datafilefinder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/datafilefinder_8h__incl.svg -> ../html-full/datafilefinder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000115_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000116_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000115_000002.xhtml -> ../html-lib/dir_000116_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/position_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h__incl.svg -> ../html-full/position_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairlistSets.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PairlistSets.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairlistSets.xhtml -> ../html-lib/classgmx_1_1PairlistSets.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1RocfftPlan.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan.xhtml -> ../html-lib/structgmx_1_1RocfftPlan.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plot_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h.xhtml -> ../html-lib/plot_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ArrayRefWithPadding-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ArrayRefWithPadding-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ArrayRefWithPadding-members.xhtml -> ../html-full/classgmx_1_1ArrayRefWithPadding-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter.xhtml -> ../html-full/classgmx_1_1IFrameConverter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/resall_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/resall_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/resall_8h__incl.svg -> ../html-lib/resall_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/baseversion_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/baseversion_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/baseversion_8h.xhtml -> ../html-lib/baseversion_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabs.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tabs.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabs.css -> ../html-full/tabs.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_n.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_n.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_n.xhtml -> ../html-lib/namespacemembers_n.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/com_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h__incl.svg -> ../html-full/com_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000111_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000112_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000111_000002.xhtml -> ../html-lib/dir_000112_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork.xhtml -> ../html-lib/structgmx_1_1NbnxmPairlistCpuWork.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData.xhtml -> ../html-full/classgmx_1_1PotentialPointData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000054_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000054_000002.xhtml -> ../html-lib/dir_000054_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GridDimensions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions.xhtml -> ../html-lib/structgmx_1_1GridDimensions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/seed_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h.xhtml -> ../html-lib/seed_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/indexutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/indexutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/indexutil_8h__incl.svg -> ../html-full/indexutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainerwithsections_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioptionscontainerwithsections_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainerwithsections_8h__incl.svg -> ../html-full/ioptionscontainerwithsections_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000141_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000002.xhtml -> ../html-lib/dir_000141_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pargs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pargs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pargs_8h__incl.svg -> ../html-full/pargs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h.xhtml -> ../html-lib/average_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h.xhtml -> ../html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000084.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000083.xhtml -> ../html-lib/dir_000009_000084.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbsearch_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h.xhtml -> ../html-lib/nbsearch_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangePartitioning.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangePartitioning.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangePartitioning.xhtml -> ../html-full/classgmx_1_1RangePartitioning.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000058_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000058_000002.xhtml -> ../html-full/dir_000059_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PackedJClusterList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PackedJClusterList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PackedJClusterList.xhtml -> ../html-full/classgmx_1_1PackedJClusterList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ITopologyProvider.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider.xhtml -> ../html-lib/classgmx_1_1ITopologyProvider.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleSerial__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial__inherit__graph.svg -> ../html-lib/classgmx_1_1AnalysisDataModuleSerial__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryFileOpener.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener.xhtml -> ../html-lib/classgmx_1_1TrajectoryFileOpener.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_5.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_3.svg -> ../html-full/dot_inline_dotgraph_5.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitManager.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitManager.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitManager.xhtml -> ../html-lib/classgmx_1_1TimeUnitManager.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000108_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000109_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000108_000002.xhtml -> ../html-full/dir_000109_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/coordinatefile_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinatefile_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/coordinatefile_8h.xhtml -> ../html-lib/coordinatefile_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_4.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_2.svg -> ../html-full/dot_inline_dotgraph_4.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1JClusterList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1JClusterList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1JClusterList.xhtml -> ../html-full/classgmx_1_1JClusterList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommBackward-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainCommBackward-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommBackward-members.xhtml -> ../html-full/classgmx_1_1DomainCommBackward-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/symtab_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/symtab_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/symtab_8h__incl.svg -> ../html-full/symtab_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/programcontext_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h.xhtml -> ../html-lib/programcontext_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64Fast-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__sparsematrix.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__sparsematrix.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__sparsematrix.xhtml -> ../html-full/structgmx__sparsematrix.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/valuestore_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/valuestore_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/valuestore_8h__incl.svg -> ../html-full/valuestore_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/com_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h.xhtml -> ../html-lib/com_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml -> ../html-full/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution-members.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPbcAiuc.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPbcAiuc.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPbcAiuc.xhtml -> ../html-full/structPbcAiuc.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t.xhtml -> ../html-full/structgmx__ffparams__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenameoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__incl.svg -> ../html-full/filenameoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPointSetRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataPointSetRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioptionscontainer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainer_8h__incl.svg -> ../html-full/ioptionscontainer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NNPotTopologyPreprocessor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NNPotTopologyPreprocessor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NNPotTopologyPreprocessor-members.xhtml -> ../html-lib/classgmx_1_1NNPotTopologyPreprocessor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000121_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000002.xhtml -> ../html-lib/dir_000121_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformrealdistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h.xhtml -> ../html-lib/uniformrealdistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IAnalysisDataModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule-members.xhtml -> ../html-full/classgmx_1_1IAnalysisDataModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h.xhtml -> ../html-lib/selection_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t.xhtml -> ../html-full/structgmx__moltype__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1EnergyFunctionProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnergyFunctionProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1EnergyFunctionProperties-members.xhtml -> ../html-full/structgmx_1_1EnergyFunctionProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml -> ../html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ListOfLists-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists-members.xhtml -> ../html-full/classgmx_1_1ListOfLists-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000081_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000002.xhtml -> ../html-lib/dir_000081_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__interaction__function.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function.xhtml -> ../html-full/structt__interaction__function.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForceHelperBuffers.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers.xhtml -> ../html-full/classForceHelperBuffers.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/errorcodes_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/errorcodes_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/errorcodes_8h.xhtml -> ../html-lib/errorcodes_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000164_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000165_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000164_000002.xhtml -> ../html-lib/dir_000165_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> ../html-full/classgmx_1_1MissingElementConnectionError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threefry_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h.xhtml -> ../html-lib/threefry_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError-members.xhtml -> ../html-full/classgmx_1_1InconsistentInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputselector_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h.xhtml -> ../html-lib/outputselector_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1InstallationPrefixInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo.xhtml -> ../html-full/structgmx_1_1InstallationPrefixInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> ../html-full/classgmx_1_1ElementNotFoundError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError-members.xhtml -> ../html-full/classgmx_1_1ParallelConsistencyError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> ../html-full/classgmx_1_1InvalidInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError-members.xhtml -> ../html-full/classgmx_1_1CheckpointError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbcenums_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> ../html-lib/pbcenums_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000112_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000113_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000112_000002.xhtml -> ../html-lib/dir_000113_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError-members.xhtml -> ../html-full/classgmx_1_1NotImplementedError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/register_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h.xhtml -> ../html-full/register_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabulatednormaldistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h.xhtml -> ../html-lib/tabulatednormaldistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setatoms_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h.xhtml -> ../html-lib/setatoms_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> ../html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution-members.xhtml -> ../html-full/classgmx_1_1NormalDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution-members.xhtml -> ../html-full/classgmx_1_1GammaDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setprecision_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h.xhtml -> ../html-lib/setprecision_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError-members.xhtml -> ../html-full/classgmx_1_1SimulationInstabilityError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fixedcapacityvector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fixedcapacityvector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fixedcapacityvector_8h__incl.svg -> ../html-full/fixedcapacityvector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput.xhtml -> ../html-full/classgmx_1_1LegacyInput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution-members.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError-members.xhtml -> ../html-full/classgmx_1_1ModularSimulatorError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter__inherit__graph.svg -> ../html-full/classgmx_1_1IOutputAdapter__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError-members.xhtml -> ../html-full/classgmx_1_1UserInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c7469e0bc32a5001ddd4092216283533.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c7469e0bc32a5001ddd4092216283533.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c7469e0bc32a5001ddd4092216283533.xhtml -> ../html-full/dir_c7469e0bc32a5001ddd4092216283533.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__ilist.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__ilist.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__ilist.xhtml -> ../html-full/structt__ilist.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000017_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000017_000002.xhtml -> ../html-full/dir_000017_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError-members.xhtml -> ../html-full/classgmx_1_1ToleranceError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError-members.xhtml -> ../html-full/classgmx_1_1InternalError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Range_1_1iterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1Range_1_1iterator-members.xhtml -> ../html-full/structgmx_1_1Range_1_1iterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError-members.xhtml -> ../html-full/classgmx_1_1FileIOError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setstarttime_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setstarttime_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setstarttime_8h.xhtml -> ../html-lib/setstarttime_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectioncollection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h.xhtml -> ../html-lib/selectioncollection_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError-members.xhtml -> ../html-full/classgmx_1_1RangeError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/settimestep_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/settimestep_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/settimestep_8h.xhtml -> ../html-lib/settimestep_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setforces_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setforces_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setforces_8h.xhtml -> ../html-lib/setforces_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError-members.xhtml -> ../html-full/classgmx_1_1APIError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__sci__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__sci__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__sci__t.xhtml -> ../html-full/structgmx_1_1nbnxn__sci__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionenums_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionenums_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionenums_8h.xhtml -> ../html-lib/selectionenums_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setvelocities_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setvelocities_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setvelocities_8h.xhtml -> ../html-lib/setvelocities_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExceptionInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExceptionInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExceptionInfo.xhtml -> ../html-lib/classgmx_1_1ExceptionInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_n.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_n.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_n.xhtml -> ../html-lib/namespacemembers_func_n.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioutputadapter_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioutputadapter_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioutputadapter_8h.xhtml -> ../html-lib/ioutputadapter_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arraydata_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h.xhtml -> ../html-lib/arraydata_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoption_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h.xhtml -> ../html-lib/selectionoption_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_9.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_4.svg -> ../html-full/msc_inline_mscgraph_9.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataValue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataValue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setbox_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setbox_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setbox_8h.xhtml -> ../html-lib/setbox_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000127_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000128_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000127_000002.xhtml -> ../html-lib/dir_000128_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dynsections.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dynsections.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dynsections.js -> ../html-full/dynsections.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel-members.xhtml -> ../html-full/classgmx_1_1TorchModel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionPosition-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionPosition-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionPosition-members.xhtml -> ../html-full/classgmx_1_1SelectionPosition-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/datafilefinder_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datafilefinder_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/datafilefinder_8h.xhtml -> ../html-lib/datafilefinder_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomentum.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum.xhtml -> ../html-full/structSystemMomentum.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoption_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h.xhtml -> ../html-lib/filenameoption_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/displacement_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/displacement_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/displacement_8h.xhtml -> ../html-lib/displacement_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structMoleculeBlockIndices.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeBlockIndices.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structMoleculeBlockIndices.xhtml -> ../html-full/structMoleculeBlockIndices.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysisdata_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h.xhtml -> ../html-lib/analysisdata_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structdf__history__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structdf__history__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structdf__history__t-members.xhtml -> ../html-full/structdf__history__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractsection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h.xhtml -> ../html-lib/abstractsection_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection.xhtml -> ../html-lib/classgmx_1_1OptionSection.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lifetime_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h.xhtml -> ../html-lib/lifetime_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/timeunitmanager_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h.xhtml -> ../html-lib/timeunitmanager_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_6.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_4.svg -> ../html-full/dot_inline_dotgraph_6.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialdistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h.xhtml -> ../html-lib/exponentialdistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GromacsException-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GromacsException-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GromacsException-members.xhtml -> ../html-full/classgmx_1_1GromacsException-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2options_2options_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2options_2options_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2options_2options_8h.xhtml -> ../html-lib/api_2legacy_2include_2gromacs_2options_2options_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/requirements_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/requirements_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/requirements_8h.xhtml -> ../html-lib/requirements_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignal.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignal.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignal.xhtml -> ../html-full/classgmx_1_1SimulationSignal.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/normaldistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h.xhtml -> ../html-lib/normaldistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> ../html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/init_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/init_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/init_8h.xhtml -> ../html-lib/init_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gammadistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h.xhtml -> ../html-lib/gammadistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/alignedallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/alignedallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/alignedallocator_8h__incl.svg -> ../html-full/alignedallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForeignLambdaTerms-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForeignLambdaTerms-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForeignLambdaTerms-members.xhtml -> ../html-full/classForeignLambdaTerms-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/graph_legend.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/graph_legend.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/graph_legend.xhtml -> ../html-full/graph_legend.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1HaloExchange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HaloExchange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1HaloExchange-members.xhtml -> ../html-full/classgmx_1_1HaloExchange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000040_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000040_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000040_000002.xhtml -> ../html-lib/dir_000040_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineinit_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineinit_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineinit_8h__incl.svg -> ../html-full/cmdlineinit_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhood-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhood-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhood-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhood-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NonbondedBenchmarkInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NonbondedBenchmarkInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NonbondedBenchmarkInfo.xhtml -> ../html-lib/classgmx_1_1NonbondedBenchmarkInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b3b10afaa073fb580ca3168487895926.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b3b10afaa073fb580ca3168487895926.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b3b10afaa073fb580ca3168487895926.xhtml -> ../html-full/dir_b3b10afaa073fb580ca3168487895926.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion-members.xhtml -> ../html-full/classgmx_1_1ProcessFrameConversion-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FlagsTemplate-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FlagsTemplate-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FlagsTemplate-members.xhtml -> ../html-full/classgmx_1_1FlagsTemplate-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__packed__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arrayref_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arrayref_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arrayref_8h__incl.svg -> ../html-full/arrayref_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__filenm.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__filenm.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__filenm.xhtml -> ../html-full/structt__filenm.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000039_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000039_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000039_000002.xhtml -> ../html-lib/dir_000039_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/range_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/range_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/range_8h__incl.svg -> ../html-full/range_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structAtomsAdjacencyListElement.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structAtomsAdjacencyListElement.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structAtomsAdjacencyListElement.xhtml -> ../html-full/structAtomsAdjacencyListElement.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000116_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000117_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000116_000002.xhtml -> ../html-lib/dir_000117_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/repeatingsection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h.xhtml -> ../html-lib/repeatingsection_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structFEPStateValue.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structFEPStateValue.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structFEPStateValue.xhtml -> ../html-full/structFEPStateValue.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setprecision_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h__incl.svg -> ../html-full/setprecision_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinerunner_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h.xhtml -> ../html-lib/cmdlinerunner_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData.xhtml -> ../html-lib/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainerWithSections-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections-members.xhtml -> ../html-full/classgmx_1_1IOptionsContainerWithSections-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/viewit_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/viewit_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/viewit_8h.xhtml -> ../html-lib/viewit_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformintdistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformintdistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformintdistribution_8h.xhtml -> ../html-lib/uniformintdistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionmanager_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h.xhtml -> ../html-lib/selectionoptionmanager_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionbehavior_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionbehavior_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionbehavior_8h.xhtml -> ../html-lib/selectionoptionbehavior_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000141_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000142_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000141_000002.xhtml -> ../html-lib/dir_000142_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000071_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000072_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000071_000002.xhtml -> ../html-full/dir_000072_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringFormatter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringFormatter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringFormatter.xhtml -> ../html-full/classgmx_1_1StringFormatter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysissettings_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h.xhtml -> ../html-lib/analysissettings_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1H5md-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1H5md-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1H5md-members.xhtml -> ../html-full/classgmx_1_1H5md-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorConfig.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorConfig.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorConfig.xhtml -> ../html-lib/structgmx_1_1SimulatorConfig.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2.xhtml -> ../html-full/structgmx_1_1StaticLog2.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainerwithsections_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainerwithsections_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainerwithsections_8h.xhtml -> ../html-lib/ioptionscontainerwithsections_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainer_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainer_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionscontainer_8h.xhtml -> ../html-lib/ioptionscontainer_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BenchmarkSystem-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem-members.xhtml -> ../html-full/structgmx_1_1BenchmarkSystem-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t.xhtml -> ../html-full/structgmx__localtop__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> ../html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000113_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000114_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000113_000002.xhtml -> ../html-lib/dir_000114_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000025_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000025_000007.xhtml -> ../html-lib/dir_000025_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SelectionTopologyProperties-members.xhtml -> ../html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputRequirementOptionDirector.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputRequirementOptionDirector.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputRequirementOptionDirector.xhtml -> ../html-lib/classgmx_1_1OutputRequirementOptionDirector.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000160_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000161_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000160_000168.xhtml -> ../html-full/dir_000161_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior-members.xhtml -> ../html-full/classgmx_1_1TimeUnitBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/template_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp.xhtml -> ../html-lib/template_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plot_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h__incl.svg -> ../html-full/plot_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Profiling.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Profiling.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Profiling.xhtml -> ../html-lib/classgmx_1_1Profiling.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionsection_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionsection_8h.xhtml -> ../html-lib/optionsection_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineModuleSettings.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineModuleSettings.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineModuleSettings.xhtml -> ../html-lib/classgmx_1_1CommandLineModuleSettings.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000104_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000105_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000104_000002.xhtml -> ../html-lib/dir_000105_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_2.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_2.svg -> ../html-full/msc_inline_mscgraph_2.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairlistSets-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PairlistSets-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairlistSets-members.xhtml -> ../html-full/classgmx_1_1PairlistSets-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector-members.xhtml -> ../html-full/classgmx_1_1OutputSelector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisArrayData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisArrayData__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisArrayData__inherit__graph.svg -> ../html-lib/classgmx_1_1AbstractAnalysisArrayData__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPdbAtomEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPdbAtomEntry-members.xhtml -> ../html-full/classPdbAtomEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000142_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000143_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000142_000002.xhtml -> ../html-lib/dir_000143_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities-members.xhtml -> ../html-full/classgmx_1_1SetVelocities-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/graph_legend.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/graph_legend.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/graph_legend.svg -> ../html-full/graph_legend.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000126_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000127_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000126_000002.xhtml -> ../html-lib/dir_000127_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000081_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000169.xhtml -> ../html-lib/dir_000081_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime-members.xhtml -> ../html-full/classgmx_1_1SetStartTime-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000149_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000150_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000149_000002.xhtml -> ../html-lib/dir_000150_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep-members.xhtml -> ../html-full/classgmx_1_1SetTimeStep-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000124_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000125_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000124_000002.xhtml -> ../html-lib/dir_000125_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision-members.xhtml -> ../html-full/classgmx_1_1SetPrecision-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractoption_8h__incl.svg -> ../html-full/abstractoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PairSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PairSearch-members.xhtml -> ../html-full/classgmx_1_1PairSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fileptr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fileptr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fileptr_8h__incl.svg -> ../html-full/fileptr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1INNPotModel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel-members.xhtml -> ../html-full/classgmx_1_1INNPotModel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000154_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000155_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000154_000002.xhtml -> ../html-lib/dir_000155_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms-members.xhtml -> ../html-full/classgmx_1_1SetAtoms-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta.xhtml -> ../html-full/structSystemMomenta.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__excl__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__excl__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__excl__t.xhtml -> ../html-full/structgmx_1_1nbnxn__excl__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BoolType.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BoolType.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BoolType.xhtml -> ../html-lib/structgmx_1_1BoolType.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox-members.xhtml -> ../html-full/classgmx_1_1SetBox-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces-members.xhtml -> ../html-full/classgmx_1_1SetForces-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionsbehavior_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h__dep__incl.svg -> ../html-lib/ioptionsbehavior_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_11_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_11_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_11_dark.png -> ../html-full/form_11_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextLineWrapper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper-members.xhtml -> ../html-full/classgmx_1_1TextLineWrapper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1nbnxn__cycle__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1nbnxn__cycle__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1nbnxn__cycle__t.xhtml -> ../html-lib/classgmx_1_1nbnxn__cycle__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__molblock__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__molblock__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__molblock__t.xhtml -> ../html-full/structgmx__molblock__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExceptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExceptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExceptionInfo-members.xhtml -> ../html-lib/classgmx_1_1ExceptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionfiletype_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionfiletype_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionfiletype_8h.xhtml -> ../html-lib/optionfiletype_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConvertTprInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo.xhtml -> ../html-full/classgmx_1_1ConvertTprInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OutputRequirements-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1OutputRequirements-members.xhtml -> ../html-full/structgmx_1_1OutputRequirements-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager-members.xhtml -> ../html-full/classgmx_1_1FileNameOptionManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSettleWaterTopology.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSettleWaterTopology.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSettleWaterTopology.xhtml -> ../html-full/structSettleWaterTopology.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1RocfftPlan-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1RocfftPlan-members.xhtml -> ../html-full/structgmx_1_1RocfftPlan-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoptionmanager_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoptionmanager_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoptionmanager_8h.xhtml -> ../html-lib/filenameoptionmanager_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000087_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000088_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000087_000002.xhtml -> ../html-lib/dir_000088_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MembedHolder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MembedHolder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MembedHolder-members.xhtml -> ../html-full/classgmx_1_1MembedHolder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisHistogramSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisHistogramSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisHistogramSettings-members.xhtml -> ../html-full/classgmx_1_1AnalysisHistogramSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classWarningHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classWarningHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classWarningHandler-members.xhtml -> ../html-full/classWarningHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_1.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_1.svg -> ../html-full/msc_inline_mscgraph_1.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000092.xhtml -> ../html-lib/dir_000023_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/allocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/allocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/allocator_8h__incl.svg -> ../html-full/allocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PackedJClusterList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PackedJClusterList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PackedJClusterList-members.xhtml -> ../html-full/classgmx_1_1PackedJClusterList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/register_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h__incl.svg -> ../html-full/register_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_11.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_11.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_11.png -> ../html-full/form_11.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping.xhtml -> ../html-full/structt__mapping.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__im__ei__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t.xhtml -> ../html-full/structgmx_1_1nbnxn__im__ei__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo.xhtml -> ../html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000138_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000139_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000138_000002.xhtml -> ../html-lib/dir_000139_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommForward-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainCommForward-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainCommForward-members.xhtml -> ../html-full/classgmx_1_1DomainCommForward-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions-members.xhtml -> ../html-full/classInteractionDefinitions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000084.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000083.xhtml -> ../html-lib/dir_000120_000084.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior-members.xhtml -> ../html-full/classgmx_1_1SelectionOptionBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GromppMtsOpts.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GromppMtsOpts.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GromppMtsOpts.xhtml -> ../html-full/structgmx_1_1GromppMtsOpts.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputadapters_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h.xhtml -> ../html-lib/outputadapters_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1CompileTimeStringJoin.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CompileTimeStringJoin.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1CompileTimeStringJoin.xhtml -> ../html-full/structgmx_1_1CompileTimeStringJoin.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__matrix-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__matrix-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__matrix-members.xhtml -> ../html-full/structt__matrix-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionsbehavior_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioptionsbehavior_8h.xhtml -> ../html-lib/ioptionsbehavior_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineparser_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h.xhtml -> ../html-lib/cmdlineparser_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PairsearchWork-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PairsearchWork-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PairsearchWork-members.xhtml -> ../html-full/structgmx_1_1PairsearchWork-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpwriter_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h.xhtml -> ../html-lib/cmdlinehelpwriter_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/enumerationhelpers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/enumerationhelpers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/enumerationhelpers_8h__incl.svg -> ../html-full/enumerationhelpers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__pargs-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__pargs-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__pargs-members.xhtml -> ../html-full/structt__pargs-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_7.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_12.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_7.svg -> ../html-full/msc_inline_mscgraph_12.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__pbc-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__pbc-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__pbc-members.xhtml -> ../html-full/structt__pbc-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/menu.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/menu.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/menu.js -> ../html-full/menu.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1JClusterList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1JClusterList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1JClusterList-members.xhtml -> ../html-full/classgmx_1_1JClusterList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotSettings-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataPlotSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineHelpWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineHelpWriter-members.xhtml -> ../html-full/classgmx_1_1CommandLineHelpWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlanSetupData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData.xhtml -> ../html-lib/structgmx_1_1PlanSetupData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000025_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000025_000092.xhtml -> ../html-full/dir_000025_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setstarttime_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setstarttime_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setstarttime_8h__incl.svg -> ../html-full/setstarttime_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/settimestep_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/settimestep_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/settimestep_8h__incl.svg -> ../html-full/settimestep_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorStateData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulatorStateData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorStateData-members.xhtml -> ../html-full/structgmx_1_1SimulatorStateData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nonbonded__bench_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h__incl.svg -> ../html-full/nonbonded__bench_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyGroupsPerCluster-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyGroupsPerCluster-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyGroupsPerCluster-members.xhtml -> ../html-full/classgmx_1_1EnergyGroupsPerCluster-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml -> ../html-full/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/functions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_8h__incl.svg -> ../html-full/functions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/idef_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/idef_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/idef_8h__incl.svg -> ../html-full/idef_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GridDimensions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions-members.xhtml -> ../html-full/structgmx_1_1GridDimensions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000043_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000043_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000043_000002.xhtml -> ../html-full/dir_000043_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000045_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000045_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000045_000002.xhtml -> ../html-full/dir_000045_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PullCoordExpressionParser.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PullCoordExpressionParser.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PullCoordExpressionParser.xhtml -> ../html-lib/classgmx_1_1PullCoordExpressionParser.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError__inherit__graph.svg -> ../html-full/classgmx_1_1ModularSimulatorError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineModule-members.xhtml -> ../html-full/classgmx_1_1ICommandLineModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000146_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000147_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000146_000002.xhtml -> ../html-lib/dir_000147_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000006_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000062.xhtml -> ../html-lib/dir_000006_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitManager-members.xhtml -> ../html-full/classgmx_1_1TimeUnitManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysissettings_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h__incl.svg -> ../html-full/analysissettings_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOutputAdapter-members.xhtml -> ../html-full/classgmx_1_1IOutputAdapter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_16.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16.png -> ../html-full/form_16.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulatorEnv-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulatorEnv-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulatorEnv-members.xhtml -> ../html-full/classgmx_1_1SimulatorEnv-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionManager.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager.xhtml -> ../html-lib/classgmx_1_1IOptionManager.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__nodecomm__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__nodecomm__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__nodecomm__t.xhtml -> ../html-full/structgmx__nodecomm__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__index__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__index__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__index__t.xhtml -> ../html-full/structgmx__ana__index__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainerWithSections__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections__inherit__graph.svg -> ../html-lib/classgmx_1_1IOptionsContainerWithSections__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IProgramContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IProgramContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IProgramContext-members.xhtml -> ../html-full/classgmx_1_1IProgramContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setvelocities_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setvelocities_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setvelocities_8h__incl.svg -> ../html-full/setvelocities_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainer__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainer__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainer__inherit__graph.svg -> ../html-lib/classgmx_1_1IOptionsContainer__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameHeader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameHeader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameHeader-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameHeader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setforces_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setforces_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setforces_8h__incl.svg -> ../html-full/setforces_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classt__nblist-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__nblist-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classt__nblist-members.xhtml -> ../html-full/classt__nblist-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Range-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Range-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Range-members.xhtml -> ../html-full/classgmx_1_1Range-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000029_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000029_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000029_000002.xhtml -> ../html-full/dir_000029_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000031_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000031_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000031_000002.xhtml -> ../html-full/dir_000031_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structWaterMolecule.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structWaterMolecule.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structWaterMolecule.xhtml -> ../html-full/structWaterMolecule.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignaller-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignaller-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignaller-members.xhtml -> ../html-full/classgmx_1_1SimulationSignaller-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__t.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1MtsLevel.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MtsLevel.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1MtsLevel.xhtml -> ../html-full/structgmx_1_1MtsLevel.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nonbonded__bench_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nonbonded__bench_8h.xhtml -> ../html-lib/nonbonded__bench_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionList-members.xhtml -> ../html-full/structInteractionList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_16_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_16_dark.png -> ../html-full/form_16_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000096_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000097_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000096_000168.xhtml -> ../html-full/dir_000097_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangePartitioning-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangePartitioning-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangePartitioning-members.xhtml -> ../html-full/classgmx_1_1RangePartitioning-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t-members.xhtml -> ../html-full/structgmx__moltype__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000092.xhtml -> ../html-full/dir_000065_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000059_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000060_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000059_000002.xhtml -> ../html-full/dir_000060_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/utility_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/utility_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/utility_8h.xhtml -> ../html-full/utility_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000086_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000086_000002.xhtml -> ../html-full/dir_000087_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IRestraintPotential-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IRestraintPotential-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IRestraintPotential-members.xhtml -> ../html-full/classgmx_1_1IRestraintPotential-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraysize_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arraysize_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraysize_8h.xhtml -> ../html-lib/arraysize_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineprogramcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineprogramcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineprogramcontext_8h__incl.svg -> ../html-full/cmdlineprogramcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml -> ../html-full/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainer-members.xhtml -> ../html-full/classgmx_1_1IOptionsContainer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__pos__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__pos__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__pos__t-members.xhtml -> ../html-full/structgmx__ana__pos__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef-members.xhtml -> ../html-full/structt__idef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000081_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000082_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000081_000168.xhtml -> ../html-full/dir_000082_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DataFileFinder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DataFileFinder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DataFileFinder-members.xhtml -> ../html-full/classgmx_1_1DataFileFinder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000000_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000000_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000000_000168.xhtml -> ../html-full/dir_000000_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPbcAiuc-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPbcAiuc-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPbcAiuc-members.xhtml -> ../html-full/structPbcAiuc-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionListHandle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle.xhtml -> ../html-full/structInteractionListHandle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000167_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000092.xhtml -> ../html-lib/dir_000167_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_e3005fccce81b430ecaf4f4ae7f955ec.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e3005fccce81b430ecaf4f4ae7f955ec.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_e3005fccce81b430ecaf4f4ae7f955ec.xhtml -> ../html-lib/dir_e3005fccce81b430ecaf4f4ae7f955ec.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomProxy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomProxy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomProxy-members.xhtml -> ../html-full/classAtomProxy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arraydata_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__dep__incl.svg -> ../html-lib/arraydata_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter-members.xhtml -> ../html-full/classgmx_1_1IFrameConverter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000062.xhtml -> ../html-lib/dir_000024_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000003_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000003_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000003_000092.xhtml -> ../html-lib/dir_000003_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__sci__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__sci__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__sci__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__sci__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_010_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_010_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_010_01_4.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_010_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IdentityFormatter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IdentityFormatter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IdentityFormatter.xhtml -> ../html-full/classgmx_1_1IdentityFormatter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomsetdata_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h.xhtml -> ../html-lib/localatomsetdata_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/seed_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__incl.svg -> ../html-full/seed_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainPairComm-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainPairComm-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DomainPairComm-members.xhtml -> ../html-full/classgmx_1_1DomainPairComm-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000134_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000134_000002.xhtml -> ../html-full/dir_000135_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__indexmap__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__indexmap__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__indexmap__t-members.xhtml -> ../html-full/structgmx__ana__indexmap__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000130_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000131_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000130_000002.xhtml -> ../html-lib/dir_000131_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000078_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000079_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000078_000062.xhtml -> ../html-lib/dir_000079_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t-members.xhtml -> ../html-full/structgmx__ffparams__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineParser-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineParser-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineParser-members.xhtml -> ../html-full/classgmx_1_1CommandLineParser-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/testmodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testmodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/testmodule_8h__incl.svg -> ../html-lib/testmodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_011_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_011_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_011_01_4.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_011_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000070.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000070.xhtml -> ../html-lib/dir_000160_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmap__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmap__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmap__t.xhtml -> ../html-full/structgmx__cmap__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000111_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000112_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000111_000062.xhtml -> ../html-lib/dir_000112_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__xpmelmt.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__xpmelmt.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__xpmelmt.xhtml -> ../html-full/structt__xpmelmt.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPmeSolve-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPmeSolve-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classPmeSolve-members.xhtml -> ../html-full/classPmeSolve-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structIndexGroup.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structIndexGroup.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structIndexGroup.xhtml -> ../html-full/structIndexGroup.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__interaction__function-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function-members.xhtml -> ../html-full/structt__interaction__function-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_6.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_6.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_6.png -> ../html-full/form_6.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setbox_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setbox_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setbox_8h__incl.svg -> ../html-full/setbox_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structMoleculeBlockIndices-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeBlockIndices-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structMoleculeBlockIndices-members.xhtml -> ../html-full/structMoleculeBlockIndices-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_v.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_v.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_v.xhtml -> ../html-lib/namespacemembers_v.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cstringutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cstringutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cstringutil_8h__incl.svg -> ../html-full/cstringutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomProperties-members.xhtml -> ../html-full/classAtomProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__enerdata__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__enerdata__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__enerdata__t-members.xhtml -> ../html-full/structgmx__enerdata__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_6_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_6_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_6_dark.png -> ../html-full/form_6_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml -> ../html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000054_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000054_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000054_000169.xhtml -> ../html-full/dir_000054_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000020_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000020_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000020_000168.xhtml -> ../html-full/dir_000020_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/unique__cptr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/unique__cptr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/unique__cptr_8h__incl.svg -> ../html-full/unique__cptr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput-members.xhtml -> ../html-full/classgmx_1_1LegacyInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structLocalSettleData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structLocalSettleData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structLocalSettleData.xhtml -> ../html-full/structLocalSettleData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineModuleSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineModuleSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CommandLineModuleSettings-members.xhtml -> ../html-full/classgmx_1_1CommandLineModuleSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_h.xhtml -> ../html-lib/namespacemembers_func_h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_2a7e973503d881e60df68eed40a2f16a.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_2a7e973503d881e60df68eed40a2f16a.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_2a7e973503d881e60df68eed40a2f16a.xhtml -> ../html-full/dir_2a7e973503d881e60df68eed40a2f16a.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/isectionstorage_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/isectionstorage_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/isectionstorage_8h.xhtml -> ../html-lib/isectionstorage_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior-members.xhtml -> ../html-full/classgmx_1_1IOptionsBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml -> ../html-full/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineoptionsmodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineoptionsmodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineoptionsmodule_8h__incl.svg -> ../html-full/cmdlineoptionsmodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1gmx__cache__protect__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1gmx__cache__protect__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1gmx__cache__protect__t.xhtml -> ../html-full/structgmx_1_1gmx__cache__protect__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__kernel__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hip__kernel__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__kernel__utils_8h__incl.svg -> ../html-full/hip__kernel__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_8.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_13.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_8.svg -> ../html-full/msc_inline_mscgraph_13.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EqualCaseInsensitive.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EqualCaseInsensitive.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EqualCaseInsensitive.xhtml -> ../html-full/classgmx_1_1EqualCaseInsensitive.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1CompileTimeStringJoin-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CompileTimeStringJoin-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1CompileTimeStringJoin-members.xhtml -> ../html-full/structgmx_1_1CompileTimeStringJoin-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForceHelperBuffers-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers-members.xhtml -> ../html-full/classForceHelperBuffers-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> ../html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/isectionstorage_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/isectionstorage_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/isectionstorage_8h__dep__incl.svg -> ../html-lib/isectionstorage_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorConfig-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulatorConfig-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1SimulatorConfig-members.xhtml -> ../html-full/structgmx_1_1SimulatorConfig-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_af3696197bf82a93bf282a2e5bb38332.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_af3696197bf82a93bf282a2e5bb38332.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_af3696197bf82a93bf282a2e5bb38332.xhtml -> ../html-full/dir_af3696197bf82a93bf282a2e5bb38332.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_09141f8584d4385ef272b4a84e5b3373.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_09141f8584d4385ef272b4a84e5b3373.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_09141f8584d4385ef272b4a84e5b3373.xhtml -> ../html-full/dir_09141f8584d4385ef272b4a84e5b3373.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_d01c07398b4254f96a7150c96b79b270.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_d01c07398b4254f96a7150c96b79b270.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_d01c07398b4254f96a7150c96b79b270.xhtml -> ../html-full/dir_d01c07398b4254f96a7150c96b79b270.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_15_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_15_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_15_dark.png -> ../html-full/form_15_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml -> ../html-full/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData-members.xhtml -> ../html-full/classgmx_1_1PotentialPointData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000114_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000115_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000114_000002.xhtml -> ../html-lib/dir_000115_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConstraintsParam-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConstraintsParam-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConstraintsParam-members.xhtml -> ../html-full/classgmx_1_1ConstraintsParam-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_10_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10_dark.png -> ../html-full/form_10_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structFEPStateValue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structFEPStateValue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structFEPStateValue-members.xhtml -> ../html-full/structFEPStateValue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1nbnxn__cycle__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1nbnxn__cycle__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1nbnxn__cycle__t-members.xhtml -> ../html-full/classgmx_1_1nbnxn__cycle__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_31_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18_dark.png -> ../html-full/form_31_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> ../html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformrealdistribution_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniformrealdistribution_8h__dep__incl.svg -> ../html-lib/uniformrealdistribution_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/stringutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/stringutil_8h__incl.svg -> ../html-full/stringutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_31.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_18.png -> ../html-full/form_31.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenm_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenm_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenm_8h__incl.svg -> ../html-full/filenm_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DataFileInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DataFileInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DataFileInfo-members.xhtml -> ../html-full/structgmx_1_1DataFileInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TopologyData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TopologyData-members.xhtml -> ../html-full/classgmx_1_1TopologyData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/displacement_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/displacement_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/displacement_8h__incl.svg -> ../html-full/displacement_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignal-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignal-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationSignal-members.xhtml -> ../html-full/classgmx_1_1SimulationSignal-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000061_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000062_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000061_000168.xhtml -> ../html-full/dir_000062_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomentum-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomentum-members.xhtml -> ../html-full/structSystemMomentum-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_8c428f345b527d2071b666c6f8374398.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c428f345b527d2071b666c6f8374398.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_8c428f345b527d2071b666c6f8374398.xhtml -> ../html-full/dir_8c428f345b527d2071b666c6f8374398.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000143_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000144_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000143_000002.xhtml -> ../html-full/dir_000144_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_14_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_14_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_14_dark.png -> ../html-full/form_14_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000121_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000122_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000121_000002.xhtml -> ../html-lib/dir_000122_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Profiling-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Profiling-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Profiling-members.xhtml -> ../html-full/classgmx_1_1Profiling-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structAtomsAdjacencyListElement-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structAtomsAdjacencyListElement-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structAtomsAdjacencyListElement-members.xhtml -> ../html-full/structAtomsAdjacencyListElement-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_27_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_40_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_27_dark.png -> ../html-full/form_40_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_10.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_10.png -> ../html-full/form_10.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000118_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000119_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000118_000002.xhtml -> ../html-lib/dir_000119_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000065_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000065_000092.xhtml -> ../html-lib/dir_000066_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_15.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_15.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_15.png -> ../html-full/form_15.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000127_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000128_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000127_000062.xhtml -> ../html-lib/dir_000128_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BoolType-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BoolType-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BoolType-members.xhtml -> ../html-full/structgmx_1_1BoolType-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000045.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000141_000045.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000140_000045.xhtml -> ../html-lib/dir_000141_000045.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringToEnumValueConverter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringToEnumValueConverter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringToEnumValueConverter-members.xhtml -> ../html-full/classgmx_1_1StringToEnumValueConverter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000009.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000167_000009.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000166_000009.xhtml -> ../html-lib/dir_000167_000009.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_14.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_14.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_14.png -> ../html-full/form_14.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ITopologyProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ITopologyProvider-members.xhtml -> ../html-full/classgmx_1_1ITopologyProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1beec4451a575fca81beb42517047512.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1beec4451a575fca81beb42517047512.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1beec4451a575fca81beb42517047512.xhtml -> ../html-full/dir_1beec4451a575fca81beb42517047512.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__sparsematrix-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__sparsematrix-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__sparsematrix-members.xhtml -> ../html-full/structgmx__sparsematrix-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFileOpener-members.xhtml -> ../html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1InstallationPrefixInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo-members.xhtml -> ../html-full/structgmx_1_1InstallationPrefixInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml -> ../html-full/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/testmodule_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testmodule_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/testmodule_8h.xhtml -> ../html-lib/testmodule_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/timeunitmanager_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__dep__incl.svg -> ../html-lib/timeunitmanager_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__ilist-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__ilist-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__ilist-members.xhtml -> ../html-full/structt__ilist-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000075_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000076_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000075_000092.xhtml -> ../html-lib/dir_000076_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000131_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000132_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000131_000062.xhtml -> ../html-lib/dir_000132_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000096_000081.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000097_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000096_000081.xhtml -> ../html-full/dir_000097_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__packed__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml -> ../html-full/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_27.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_40.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_27.png -> ../html-full/form_40.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConvertTprInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ConvertTprInfo-members.xhtml -> ../html-full/classgmx_1_1ConvertTprInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__excl__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__excl__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__excl__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__excl__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__filenm-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__filenm-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__filenm-members.xhtml -> ../html-full/structt__filenm-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSimulationGroups-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSimulationGroups-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSimulationGroups-members.xhtml -> ../html-full/structSimulationGroups-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> ../html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbcenums_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h__dep__incl.svg -> ../html-lib/pbcenums_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000058_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000058_000169.xhtml -> ../html-full/dir_000059_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__nodecomm__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__nodecomm__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__nodecomm__t-members.xhtml -> ../html-full/structgmx__nodecomm__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000070.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000134_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000070.xhtml -> ../html-lib/dir_000134_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000152_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000007.xhtml -> ../html-lib/dir_000152_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000075_000009.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000076_000009.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000075_000009.xhtml -> ../html-lib/dir_000076_000009.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSettleWaterTopology-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSettleWaterTopology-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSettleWaterTopology-members.xhtml -> ../html-full/structSettleWaterTopology-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml -> ../html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GromppMtsOpts-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GromppMtsOpts-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GromppMtsOpts-members.xhtml -> ../html-full/structgmx_1_1GromppMtsOpts-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml -> ../html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PlanSetupData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PlanSetupData-members.xhtml -> ../html-full/structgmx_1_1PlanSetupData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PullCoordExpressionParser-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PullCoordExpressionParser-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PullCoordExpressionParser-members.xhtml -> ../html-full/classgmx_1_1PullCoordExpressionParser-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml -> ../html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml -> ../html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__nblist_1_1IEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1IEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__nblist_1_1IEntry-members.xhtml -> ../html-full/structt__nblist_1_1IEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__molblock__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__molblock__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__molblock__t-members.xhtml -> ../html-full/structgmx__molblock__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000073_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000092.xhtml -> ../html-lib/dir_000073_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputRequirementOptionDirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputRequirementOptionDirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputRequirementOptionDirector-members.xhtml -> ../html-full/classgmx_1_1OutputRequirementOptionDirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000004_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000004_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000004_000092.xhtml -> ../html-lib/dir_000004_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000163_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000164_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000163_000168.xhtml -> ../html-full/dir_000164_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/topologyinformation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/topologyinformation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/topologyinformation_8h__incl.svg -> ../html-full/topologyinformation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/boundingbox_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boundingbox_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/boundingbox_8h.xhtml -> ../html-lib/boundingbox_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_4.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_4.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_4.png -> ../html-full/form_4.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFrameWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryFrameWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TrajectoryFrameWriter-members.xhtml -> ../html-full/classgmx_1_1TrajectoryFrameWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000022_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000022_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000022_000002.xhtml -> ../html-full/dir_000022_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000084_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000085_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000084_000168.xhtml -> ../html-full/dir_000085_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringFormatter-members.xhtml -> ../html-full/classgmx_1_1StringFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml -> ../html-full/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_7e013631519469366ffd6bf609372539.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7e013631519469366ffd6bf609372539.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_7e013631519469366ffd6bf609372539.xhtml -> ../html-full/dir_7e013631519469366ffd6bf609372539.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml -> ../html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml -> ../html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_22dfbea999db116fd1efebf9609d6e70.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_22dfbea999db116fd1efebf9609d6e70.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_22dfbea999db116fd1efebf9609d6e70.xhtml -> ../html-full/dir_22dfbea999db116fd1efebf9609d6e70.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BoxDeformationHandle-members.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NbnxmKernel.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NbnxmKernel.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NbnxmKernel.xhtml -> ../html-lib/classgmx_1_1NbnxmKernel.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000115_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000116_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000115_000062.xhtml -> ../html-lib/dir_000116_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_4_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_4_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_4_dark.png -> ../html-full/form_4_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000006_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000006_000092.xhtml -> ../html-lib/dir_000006_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPartialDeserializedTprFile-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPartialDeserializedTprFile-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structPartialDeserializedTprFile-members.xhtml -> ../html-full/structPartialDeserializedTprFile-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RocfftInitializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RocfftInitializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RocfftInitializer-members.xhtml -> ../html-full/classgmx_1_1RocfftInitializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000147_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000148_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000147_000002.xhtml -> ../html-lib/dir_000148_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInputHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInputHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInputHandle-members.xhtml -> ../html-lib/classgmx_1_1SimulationInputHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_2.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_2.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_2.png -> ../html-full/form_2.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000011_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000011_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000011_000002.xhtml -> ../html-lib/dir_000011_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InteractiveMD-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InteractiveMD-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InteractiveMD-members.xhtml -> ../html-full/classgmx_1_1InteractiveMD-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000149_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> ../html-lib/dir_000149_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_3_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3_dark.png -> ../html-full/form_3_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_3.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3.png -> ../html-full/form_3.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000092.xhtml -> ../html-full/dir_000160_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomRange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomRange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classAtomRange-members.xhtml -> ../html-full/classAtomRange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000064_000007.xhtml -> ../html-full/dir_000065_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000081.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000074_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000081.xhtml -> ../html-full/dir_000074_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classIListRange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListRange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classIListRange-members.xhtml -> ../html-full/classIListRange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000074_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000073_000168.xhtml -> ../html-full/dir_000074_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_5_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_5_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_5_dark.png -> ../html-full/form_5_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml -> ../html-full/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000069_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000070_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000069_000168.xhtml -> ../html-full/dir_000070_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000149_000070.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000150_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000149_000070.xhtml -> ../html-lib/dir_000150_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000116_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000117_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000116_000062.xhtml -> ../html-lib/dir_000117_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_051edbf3de11cf568168f65483ae264b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_051edbf3de11cf568168f65483ae264b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_051edbf3de11cf568168f65483ae264b.xhtml -> ../html-full/dir_051edbf3de11cf568168f65483ae264b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000146_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000145_000169.xhtml -> ../html-full/dir_000146_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_5.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_5.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_5.png -> ../html-full/form_5.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000096.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000097.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000096.xhtml -> ../html-full/dir_000166_000097.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000000_000081.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000000_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000000_000081.xhtml -> ../html-full/dir_000000_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t-members.xhtml -> ../html-full/structgmx__localtop__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000137_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000062.xhtml -> ../html-lib/dir_000137_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000019.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000019.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000019.xhtml -> ../html-full/dir_000023_000019.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classBalanceRegion-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classBalanceRegion-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classBalanceRegion-members.xhtml -> ../html-full/classBalanceRegion-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000145_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000169.xhtml -> ../html-lib/dir_000145_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_2_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_2_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_2_dark.png -> ../html-full/form_2_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IonSwapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IonSwapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IonSwapping-members.xhtml -> ../html-full/classgmx_1_1IonSwapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LennardJonesCalculator.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1HaloMpiRequests-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HaloMpiRequests-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1HaloMpiRequests-members.xhtml -> ../html-full/structgmx_1_1HaloMpiRequests-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml -> ../html-full/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__index__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__index__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__index__t-members.xhtml -> ../html-full/structgmx__ana__index__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000073_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000007.xhtml -> ../html-lib/dir_000073_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000081.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000081.xhtml -> ../html-full/dir_000166_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta-members.xhtml -> ../html-full/structSystemMomenta-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000168.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000165_000168.xhtml -> ../html-full/dir_000166_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000097_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000098_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000097_000092.xhtml -> ../html-lib/dir_000098_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classIListProxy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListProxy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classIListProxy-members.xhtml -> ../html-full/classIListProxy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/restraintpotential_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/restraintpotential_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/restraintpotential_8h__incl.svg -> ../html-full/restraintpotential_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__nblist_1_1JEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1JEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__nblist_1_1JEntry-members.xhtml -> ../html-full/structt__nblist_1_1JEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000129_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000007.xhtml -> ../html-lib/dir_000129_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000152_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000092.xhtml -> ../html-lib/dir_000152_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_v.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_v.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_v.xhtml -> ../html-lib/namespacemembers_func_v.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structWaterMolecule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structWaterMolecule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structWaterMolecule-members.xhtml -> ../html-full/structWaterMolecule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1MtsLevel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MtsLevel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1MtsLevel-members.xhtml -> ../html-full/structgmx_1_1MtsLevel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000016_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000016_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000016_000169.xhtml -> ../html-lib/dir_000016_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml -> ../html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000089_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000089_000007.xhtml -> ../html-full/dir_000090_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1AtomPair-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AtomPair-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1AtomPair-members.xhtml -> ../html-full/structgmx_1_1AtomPair-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000092.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000145_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000144_000092.xhtml -> ../html-lib/dir_000145_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DiagonalMasker.xhtml -> ../html-lib/classgmx_1_1DiagonalMasker.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000137_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000138_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000137_000026.xhtml -> ../html-lib/dir_000138_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000076_000062.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000077_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000076_000062.xhtml -> ../html-full/dir_000077_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping-members.xhtml -> ../html-full/structt__mapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EqualCaseInsensitive-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EqualCaseInsensitive-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EqualCaseInsensitive-members.xhtml -> ../html-full/classgmx_1_1EqualCaseInsensitive-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CoulombCalculator.xhtml -> ../html-full/classgmx_1_1CoulombCalculator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000093_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000092_000169.xhtml -> ../html-full/dir_000093_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structwallcc__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structwallcc__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structwallcc__t-members.xhtml -> ../html-full/structwallcc__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1IsSerializableEnum-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1IsSerializableEnum-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1IsSerializableEnum-members.xhtml -> ../html-full/structgmx_1_1IsSerializableEnum-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000084_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000085_000070.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000084_000069.xhtml -> ../html-full/dir_000085_000070.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/programcontext_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h__dep__incl.svg -> ../html-lib/programcontext_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_k.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_k.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_k.xhtml -> ../html-full/namespacemembers_k.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RocfftInitializer.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RocfftInitializer.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RocfftInitializer.xhtml -> ../html-lib/classgmx_1_1RocfftInitializer.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000022.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000120_000022.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000119_000022.xhtml -> ../html-full/dir_000120_000022.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager-members.xhtml -> ../html-full/classgmx_1_1IOptionManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IdentityFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IdentityFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IdentityFormatter-members.xhtml -> ../html-full/classgmx_1_1IdentityFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml -> ../html-full/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000121_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000007.xhtml -> ../html-lib/dir_000121_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionListHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structInteractionListHandle-members.xhtml -> ../html-full/structInteractionListHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1gmx__cache__protect__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1gmx__cache__protect__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1gmx__cache__protect__t-members.xhtml -> ../html-full/structgmx_1_1gmx__cache__protect__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000005_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000005_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000005_000026.xhtml -> ../html-lib/dir_000005_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__localtop__t__coll__graph.svg -> ../html-full/structgmx__localtop__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000070.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000129_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000128_000070.xhtml -> ../html-lib/dir_000129_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000137_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000136_000026.xhtml -> ../html-lib/dir_000137_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1StaticLog2-members.xhtml -> ../html-full/structgmx_1_1StaticLog2-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000019.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000121_000019.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000120_000019.xhtml -> ../html-lib/dir_000121_000019.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000018_000019.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000018_000019.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000018_000019.xhtml -> ../html-lib/dir_000018_000019.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structLocalSettleData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structLocalSettleData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structLocalSettleData-members.xhtml -> ../html-full/structLocalSettleData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000073_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000026.xhtml -> ../html-lib/dir_000073_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmap__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmap__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmap__t-members.xhtml -> ../html-full/structgmx__cmap__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structIndexGroup-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structIndexGroup-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structIndexGroup-members.xhtml -> ../html-full/structIndexGroup-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000017_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000017_000007.xhtml -> ../html-full/dir_000017_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000003_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000003_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000003_000007.xhtml -> ../html-lib/dir_000003_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysisdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__incl.svg -> ../html-full/analysisdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000067_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000067_000007.xhtml -> ../html-lib/dir_000068_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__xpmelmt-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__xpmelmt-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__xpmelmt-members.xhtml -> ../html-full/structt__xpmelmt-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000024_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000024_000007.xhtml -> ../html-full/dir_000024_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__dep__incl.svg -> ../html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000040_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000040_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000040_000007.xhtml -> ../html-lib/dir_000040_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError__inherit__graph.svg -> ../html-full/classgmx_1_1APIError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioutputadapter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioutputadapter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ioutputadapter_8h__incl.svg -> ../html-full/ioutputadapter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000066.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000089_000067.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000066.xhtml -> ../html-lib/dir_000089_000067.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_0.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0.png -> ../html-full/form_0.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_func_z.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func_z.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_func_z.xhtml -> ../html-lib/functions_func_z.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_z.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_z.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_z.xhtml -> ../html-lib/functions_z.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_0_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_0_dark.png -> ../html-full/form_0_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__random.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__random.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__random.svg -> ../html-full/group__module__random.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_j.xhtml -> ../html-full/namespacemembers_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmapdata__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmapdata__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__cmapdata__t-members.xhtml -> ../html-full/structgmx__cmapdata__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__domdec__constraints__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__domdec__constraints__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__domdec__constraints__t.xhtml -> ../html-lib/structgmx__domdec__constraints__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_k.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_k.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_k.xhtml -> ../html-full/namespacemembers_func_k.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__inherit__graph.svg -> ../html-full/classgmx_1_1UserInputError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_x.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_x.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_x.xhtml -> ../html-full/namespacemembers_func_x.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/timeunitmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/timeunitmanager_8h__incl.svg -> ../html-full/timeunitmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_1.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_1.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_1.png -> ../html-full/form_1.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_1_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_1_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_1_dark.png -> ../html-full/form_1_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pages.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pages.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pages.xhtml -> ../html-full/pages.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals.xhtml -> ../html-lib/globals.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionbehavior_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionbehavior_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionbehavior_8h__incl.svg -> ../html-full/selectionoptionbehavior_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func_j.xhtml -> ../html-full/namespacemembers_func_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_func.xhtml -> ../html-full/namespacemembers_func.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers.xhtml -> ../html-full/namespacemembers.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_j.xhtml -> ../html-lib/functions_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopen.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderopen.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopen.svg -> ../html-full/folderopen.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_vars_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_vars_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_vars_j.xhtml -> ../html-lib/functions_vars_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals_func.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_func.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals_func.xhtml -> ../html-lib/globals_func.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_func_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/functions_func_j.xhtml -> ../html-lib/functions_func_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basedefinitions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/basedefinitions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basedefinitions_8h__incl.svg -> ../html-full/basedefinitions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_q.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_q.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/namespacemembers_q.xhtml -> ../html-lib/namespacemembers_q.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopend.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderopend.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderopend.svg -> ../html-full/folderopend.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals_k.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_k.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/globals_k.xhtml -> ../html-lib/globals_k.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/examples.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/examples.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/examples.xhtml -> ../html-full/examples.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineparser_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineparser_8h__incl.svg -> ../html-full/cmdlineparser_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg -> ../html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_7e013631519469366ffd6bf609372539_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7e013631519469366ffd6bf609372539_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_7e013631519469366ffd6bf609372539_dep.svg -> ../html-full/dir_7e013631519469366ffd6bf609372539_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg -> ../html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_9.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_14.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_9.svg -> ../html-full/msc_inline_mscgraph_14.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__idef__coll__graph.svg -> ../html-full/structt__idef__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_3.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dot_inline_dotgraph_1.svg -> ../html-full/dot_inline_dotgraph_3.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64General__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PairsearchWork__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PairsearchWork__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1PairsearchWork__coll__graph.svg -> ../html-full/structgmx_1_1PairsearchWork__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyEnumOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyEnumOption__coll__graph.svg -> ../html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> ../html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractsection_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractsection_8h__dep__incl.svg -> ../html-lib/abstractsection_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg -> ../html-full/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/register_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h__dep__incl.svg -> ../html-lib/register_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionfiletype_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionfiletype_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionfiletype_8h__dep__incl.svg -> ../html-lib/optionfiletype_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOption__coll__graph.svg -> ../html-full/classgmx_1_1EnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOption__inherit__graph.svg -> ../html-full/classgmx_1_1EnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomsetdata_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/localatomsetdata_8h__dep__incl.svg -> ../html-lib/localatomsetdata_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_12_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_12_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_12_dark.png -> ../html-full/form_12_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__coll__graph.svg -> ../html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> ../html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> ../html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError__coll__graph.svg -> ../html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/iframeconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iframeconverter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/iframeconverter_8h__incl.svg -> ../html-full/iframeconverter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_12.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_12.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_12.png -> ../html-full/form_12.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__coll__graph.svg -> ../html-full/classgmx_1_1FloatOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOption__inherit__graph.svg -> ../html-full/classgmx_1_1FloatOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOption__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOption__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__inherit__graph.svg -> ../html-full/classgmx_1_1Int64Option__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64Option__coll__graph.svg -> ../html-full/classgmx_1_1Int64Option__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAverageHistogram__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAverageHistogram__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAverageHistogram__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAverageHistogram__coll__graph.svg -> ../html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionManager__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionManager__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOption__inherit__graph.svg -> ../html-full/classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOption__coll__graph.svg -> ../html-full/classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOption__coll__graph.svg -> ../html-full/classgmx_1_1DoubleOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOption__inherit__graph.svg -> ../html-full/classgmx_1_1DoubleOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOption__inherit__graph.svg -> ../html-full/classgmx_1_1StringOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOption__coll__graph.svg -> ../html-full/classgmx_1_1StringOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOption__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOption__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSection__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractOptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSection__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Options__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Options__inherit__graph.svg -> ../html-full/classgmx_1_1Options__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Options__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Options__coll__graph.svg -> ../html-full/classgmx_1_1Options__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOption__inherit__graph.svg -> ../html-full/classgmx_1_1BooleanOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOption__coll__graph.svg -> ../html-full/classgmx_1_1BooleanOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__energyanalysis.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__energyanalysis.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/group__module__energyanalysis.svg -> ../html-full/group__module__energyanalysis.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AbstractPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionenums_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionenums_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionenums_8h__incl.svg -> ../html-full/selectionenums_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisArrayData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisArrayData__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> ../html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError__coll__graph.svg -> ../html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError__coll__graph.svg -> ../html-full/classgmx_1_1InconsistentInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError__inherit__graph.svg -> ../html-full/classgmx_1_1InconsistentInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError__coll__graph.svg -> ../html-full/classgmx_1_1CheckpointError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError__inherit__graph.svg -> ../html-full/classgmx_1_1CheckpointError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__inherit__graph.svg -> ../html-full/classgmx_1_1InvalidInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError__coll__graph.svg -> ../html-full/classgmx_1_1InvalidInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionflags_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionflags_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/optionflags_8h__incl.svg -> ../html-full/optionflags_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError__coll__graph.svg -> ../html-full/classgmx_1_1NotImplementedError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError__inherit__graph.svg -> ../html-full/classgmx_1_1NotImplementedError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__sycl__kernel__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hip__sycl__kernel__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hip__sycl__kernel__utils_8h__incl.svg -> ../html-full/hip__sycl__kernel__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/smalloc_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/smalloc_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/smalloc_8h__incl.svg -> ../html-full/smalloc_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/simulationsignal_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationsignal_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/simulationsignal_8h__incl.svg -> ../html-full/simulationsignal_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinehelpwriter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinehelpwriter_8h__incl.svg -> ../html-full/cmdlinehelpwriter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fft_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fft_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fft_8h__incl.svg -> ../html-full/fft_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_29_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_59_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_29_dark.png -> ../html-full/form_59_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_29.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_59.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_29.png -> ../html-full/form_59.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_13_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_13_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_13_dark.png -> ../html-full/form_13_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_13.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_13.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_13.png -> ../html-full/form_13.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structSystemMomenta__coll__graph.svg -> ../html-full/structSystemMomenta__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64__coll__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GridDimensions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1GridDimensions__coll__graph.svg -> ../html-full/structgmx_1_1GridDimensions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_31_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_61_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_31_dark.png -> ../html-full/form_61_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinerunner_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__dep__incl.svg -> ../html-lib/cmdlinerunner_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysissettings_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysissettings_8h__dep__incl.svg -> ../html-lib/analysissettings_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plot_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plot_8h__dep__incl.svg -> ../html-lib/plot_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineprogramcontext_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineprogramcontext_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineprogramcontext_8h__dep__incl.svg -> ../html-lib/cmdlineprogramcontext_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/init_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/init_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/init_8h__dep__incl.svg -> ../html-lib/init_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysisdata_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__dep__incl.svg -> ../html-lib/analysisdata_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__dep__incl.svg -> ../html-lib/average_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderclosedd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderclosedd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderclosedd.svg -> ../html-full/folderclosedd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderclosed.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderclosed.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/folderclosed.svg -> ../html-full/folderclosed.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg -> ../html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialdistribution_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/exponentialdistribution_8h__dep__incl.svg -> ../html-lib/exponentialdistribution_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/normaldistribution_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/normaldistribution_8h__dep__incl.svg -> ../html-lib/normaldistribution_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> ../html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_30_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_60_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_30_dark.png -> ../html-full/form_60_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__oriresdata__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__oriresdata__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__oriresdata__coll__graph.svg -> ../html-full/structt__oriresdata__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/com_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/com_8h__dep__incl.svg -> ../html-lib/com_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg -> ../html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_31.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_61.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_31.png -> ../html-full/form_61.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/baseversion_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/baseversion_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/baseversion_8h__dep__incl.svg -> ../html-lib/baseversion_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gmxassert_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmxassert_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gmxassert_8h__incl.svg -> ../html-full/gmxassert_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/seed_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__dep__incl.svg -> ../html-lib/seed_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoption_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/filenameoption_8h__dep__incl.svg -> ../html-lib/filenameoption_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/abstractdata_8h__incl.svg -> ../html-full/abstractdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/basicoptions_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__dep__incl.svg -> ../html-lib/basicoptions_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ifunc_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ifunc_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/ifunc_8h__incl.svg -> ../html-full/ifunc_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbsearch_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nbsearch_8h__dep__incl.svg -> ../html-lib/nbsearch_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionTemplate__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionTemplate__coll__graph.svg -> ../html-full/classgmx_1_1OptionTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionTemplate__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionTemplate__inherit__graph.svg -> ../html-full/classgmx_1_1OptionTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PotentialPointData__coll__graph.svg -> ../html-full/classgmx_1_1PotentialPointData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg -> ../html-full/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> ../html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError__coll__graph.svg -> ../html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_30.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_60.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_30.png -> ../html-full/form_60.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg -> ../html-full/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__pos__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__pos__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ana__pos__t__coll__graph.svg -> ../html-full/structgmx__ana__pos__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classInteractionDefinitions__coll__graph.svg -> ../html-full/classInteractionDefinitions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1test_1_1TestSystem__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1TestSystem__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1test_1_1TestSystem__coll__graph.svg -> ../html-full/structgmx_1_1test_1_1TestSystem__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__coll__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__ffparams__t__coll__graph.svg -> ../html-full/structgmx__ffparams__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BenchmarkSystem__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1BenchmarkSystem__coll__graph.svg -> ../html-full/structgmx_1_1BenchmarkSystem__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1LegacyInput__coll__graph.svg -> ../html-full/classgmx_1_1LegacyInput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/programcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/programcontext_8h__incl.svg -> ../html-full/programcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx__moltype__t__coll__graph.svg -> ../html-full/structgmx__moltype__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> ../html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ProcessFrameConversion__coll__graph.svg -> ../html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector__inherit__graph.svg -> ../html-full/classgmx_1_1OutputSelector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OutputSelector__coll__graph.svg -> ../html-full/classgmx_1_1OutputSelector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg -> ../html-full/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mapping__coll__graph.svg -> ../html-full/structt__mapping__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IFrameConverter__inherit__graph.svg -> ../html-full/classgmx_1_1IFrameConverter__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities__inherit__graph.svg -> ../html-full/classgmx_1_1SetVelocities__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetVelocities__coll__graph.svg -> ../html-full/classgmx_1_1SetVelocities__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_23_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_36_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_23_dark.png -> ../html-full/form_36_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinemodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinemodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinemodule_8h__incl.svg -> ../html-full/cmdlinemodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionManager__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionManager__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64OptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1Int64OptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep__coll__graph.svg -> ../html-full/classgmx_1_1SetTimeStep__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetTimeStep__inherit__graph.svg -> ../html-full/classgmx_1_1SetTimeStep__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision__inherit__graph.svg -> ../html-full/classgmx_1_1SetPrecision__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetPrecision__coll__graph.svg -> ../html-full/classgmx_1_1SetPrecision__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BooleanOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_20_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_33_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_20_dark.png -> ../html-full/form_33_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime__inherit__graph.svg -> ../html-full/classgmx_1_1SetStartTime__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetStartTime__coll__graph.svg -> ../html-full/classgmx_1_1SetStartTime__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1StringOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1StringOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1StringOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces__inherit__graph.svg -> ../html-full/classgmx_1_1SetForces__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetForces__coll__graph.svg -> ../html-full/classgmx_1_1SetForces__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileNameOptionManager__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1EnumOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError__coll__graph.svg -> ../html-full/classgmx_1_1ToleranceError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ToleranceError__inherit__graph.svg -> ../html-full/classgmx_1_1ToleranceError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior__coll__graph.svg -> ../html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms__coll__graph.svg -> ../html-full/classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetAtoms__inherit__graph.svg -> ../html-full/classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/flags_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/flags_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/flags_8h__incl.svg -> ../html-full/flags_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox__coll__graph.svg -> ../html-full/classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SetBox__inherit__graph.svg -> ../html-full/classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ModularSimulatorError__coll__graph.svg -> ../html-full/classgmx_1_1ModularSimulatorError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1OptionSection__coll__graph.svg -> ../html-full/classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError__inherit__graph.svg -> ../html-full/classgmx_1_1RangeError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RangeError__coll__graph.svg -> ../html-full/classgmx_1_1RangeError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UserInputError__coll__graph.svg -> ../html-full/classgmx_1_1UserInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisData__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisData__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError__inherit__graph.svg -> ../html-full/classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InternalError__coll__graph.svg -> ../html-full/classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_25_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_38_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_25_dark.png -> ../html-full/form_38_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_20.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_33.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_20.png -> ../html-full/form_33.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1INNPotModel__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1INNPotModel__inherit__graph.svg -> ../html-full/classgmx_1_1INNPotModel__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__inherit__graph.svg -> ../html-full/classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1FileIOError__coll__graph.svg -> ../html-full/classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel__coll__graph.svg -> ../html-full/classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TorchModel__inherit__graph.svg -> ../html-full/classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_23.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_36.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_23.png -> ../html-full/form_36.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_35_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22_dark.png -> ../html-full/form_35_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1APIError__coll__graph.svg -> ../html-full/classgmx_1_1APIError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_35.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_22.png -> ../html-full/form_35.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/simulationinputhandle_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationinputhandle_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/simulationinputhandle_8h__incl.svg -> ../html-full/simulationinputhandle_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_25.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_38.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_25.png -> ../html-full/form_38.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/boundingbox_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boundingbox_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/boundingbox_8h__incl.svg -> ../html-lib/boundingbox_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_24_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_37_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_24_dark.png -> ../html-full/form_37_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/docd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/docd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/docd.svg -> ../html-full/docd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doc.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doc.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doc.svg -> ../html-full/doc.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg -> ../html-full/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_26_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_39_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_26_dark.png -> ../html-full/form_39_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg -> ../html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg -> ../html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_24.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_37.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_24.png -> ../html-full/form_37.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg -> ../html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_75.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_270.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_75.svg -> ../html-full/inherit_graph_270.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_74.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_269.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_74.svg -> ../html-full/inherit_graph_269.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_76.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_271.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_76.svg -> ../html-full/inherit_graph_271.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_26.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_39.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_26.png -> ../html-full/form_39.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_125.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_516.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_125.svg -> ../html-full/inherit_graph_516.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_126.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_517.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_126.svg -> ../html-full/inherit_graph_517.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_128.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_519.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_128.svg -> ../html-full/inherit_graph_519.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_129.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_520.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_129.svg -> ../html-full/inherit_graph_520.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_183.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_776.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_183.svg -> ../html-full/inherit_graph_776.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_73.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_268.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_73.svg -> ../html-full/inherit_graph_268.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_134.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_585.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_134.svg -> ../html-full/inherit_graph_585.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_67.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_241.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_67.svg -> ../html-full/inherit_graph_241.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_68.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_242.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_68.svg -> ../html-full/inherit_graph_242.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_87.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_303.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_87.svg -> ../html-full/inherit_graph_303.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_149.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_648.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_149.svg -> ../html-full/inherit_graph_648.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_84.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_292.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_84.svg -> ../html-full/inherit_graph_292.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_82.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_290.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_82.svg -> ../html-full/inherit_graph_290.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_185.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_779.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_185.svg -> ../html-full/inherit_graph_779.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_108.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_453.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_108.svg -> ../html-full/inherit_graph_453.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_83.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_291.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_83.svg -> ../html-full/inherit_graph_291.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_136.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_589.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_136.svg -> ../html-full/inherit_graph_589.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_155.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_654.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_155.svg -> ../html-full/inherit_graph_654.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_24.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_88.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_24.svg -> ../html-full/inherit_graph_88.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_127.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_518.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_127.svg -> ../html-full/inherit_graph_518.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_107.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_250.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_107.svg -> ../html-lib/inherit_graph_250.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_85.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_298.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_85.svg -> ../html-full/inherit_graph_298.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_92.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_357.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_92.svg -> ../html-full/inherit_graph_357.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_27.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_105.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_27.svg -> ../html-full/inherit_graph_105.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_69.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_243.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_69.svg -> ../html-full/inherit_graph_243.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_205.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_962.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_205.svg -> ../html-full/inherit_graph_962.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_29.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_107.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_29.svg -> ../html-full/inherit_graph_107.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_202.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_959.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_202.svg -> ../html-full/inherit_graph_959.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_195.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_945.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_195.svg -> ../html-full/inherit_graph_945.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_63.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_229.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_63.svg -> ../html-full/inherit_graph_229.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_95.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_367.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_95.svg -> ../html-full/inherit_graph_367.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_184.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_778.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_184.svg -> ../html-full/inherit_graph_778.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_66.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_240.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_66.svg -> ../html-full/inherit_graph_240.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_81.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_289.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_81.svg -> ../html-full/inherit_graph_289.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_78.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_278.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_78.svg -> ../html-full/inherit_graph_278.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_147.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_611.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_147.svg -> ../html-full/inherit_graph_611.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_99.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_385.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_99.svg -> ../html-full/inherit_graph_385.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_97.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_369.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_97.svg -> ../html-full/inherit_graph_369.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_28.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_106.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_28.svg -> ../html-full/inherit_graph_106.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_162.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_682.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_162.svg -> ../html-full/inherit_graph_682.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_89.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_193.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_89.svg -> ../html-lib/inherit_graph_193.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_91.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_356.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_91.svg -> ../html-full/inherit_graph_356.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_201.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_958.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_201.svg -> ../html-full/inherit_graph_958.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_204.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_961.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_204.svg -> ../html-full/inherit_graph_961.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_146.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_610.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_146.svg -> ../html-full/inherit_graph_610.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_93.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_365.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_93.svg -> ../html-full/inherit_graph_365.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_98.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_384.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_98.svg -> ../html-full/inherit_graph_384.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_49.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_159.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_49.svg -> ../html-full/inherit_graph_159.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_203.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_960.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_203.svg -> ../html-full/inherit_graph_960.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_190.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_935.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_190.svg -> ../html-full/inherit_graph_935.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_121.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_278.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_121.svg -> ../html-lib/inherit_graph_278.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_189.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_934.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_189.svg -> ../html-full/inherit_graph_934.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_94.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_366.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_94.svg -> ../html-full/inherit_graph_366.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_152.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_651.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_152.svg -> ../html-full/inherit_graph_651.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_50.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_160.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_50.svg -> ../html-full/inherit_graph_160.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_31.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_137.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_31.svg -> ../html-full/inherit_graph_137.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_36.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_143.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_36.svg -> ../html-full/inherit_graph_143.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_38.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_147.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_38.svg -> ../html-full/inherit_graph_147.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_59.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_203.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_59.svg -> ../html-full/inherit_graph_203.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_42.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_151.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_42.svg -> ../html-full/inherit_graph_151.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_44.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_153.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_44.svg -> ../html-full/inherit_graph_153.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_32.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_138.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_32.svg -> ../html-full/inherit_graph_138.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_41.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_150.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_41.svg -> ../html-full/inherit_graph_150.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_11.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_51.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_11.svg -> ../html-full/inherit_graph_51.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_154.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_653.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_154.svg -> ../html-full/inherit_graph_653.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_96.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_368.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_96.svg -> ../html-full/inherit_graph_368.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_153.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_652.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_153.svg -> ../html-full/inherit_graph_652.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_40.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_149.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_40.svg -> ../html-full/inherit_graph_149.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_34.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_140.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_34.svg -> ../html-full/inherit_graph_140.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_109.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_454.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_109.svg -> ../html-full/inherit_graph_454.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_144.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_353.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_144.svg -> ../html-lib/inherit_graph_353.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_35.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_141.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_35.svg -> ../html-full/inherit_graph_141.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_33.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_139.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_33.svg -> ../html-full/inherit_graph_139.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_39.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_148.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_39.svg -> ../html-full/inherit_graph_148.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_37.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_146.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_37.svg -> ../html-full/inherit_graph_146.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_112.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_470.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_112.svg -> ../html-full/inherit_graph_470.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_174.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_755.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_174.svg -> ../html-full/inherit_graph_755.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_197.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_513.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_197.svg -> ../html-lib/inherit_graph_513.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_182.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_775.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_182.svg -> ../html-full/inherit_graph_775.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_26.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_104.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_26.svg -> ../html-full/inherit_graph_104.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_80.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_284.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_80.svg -> ../html-full/inherit_graph_284.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_57.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_188.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_57.svg -> ../html-full/inherit_graph_188.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_21.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_83.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_21.svg -> ../html-full/inherit_graph_83.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_61.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_223.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_61.svg -> ../html-full/inherit_graph_223.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_77.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_277.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_77.svg -> ../html-full/inherit_graph_277.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_86.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_299.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_86.svg -> ../html-full/inherit_graph_299.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_172.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_723.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_172.svg -> ../html-full/inherit_graph_723.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_79.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_279.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_79.svg -> ../html-full/inherit_graph_279.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_17.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_69.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_17.svg -> ../html-full/inherit_graph_69.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_140.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_598.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_140.svg -> ../html-full/inherit_graph_598.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_106.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_249.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_106.svg -> ../html-lib/inherit_graph_249.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_23.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_87.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_23.svg -> ../html-full/inherit_graph_87.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_103.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_424.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_103.svg -> ../html-full/inherit_graph_424.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_135.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_588.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_135.svg -> ../html-full/inherit_graph_588.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_199.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_954.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_199.svg -> ../html-full/inherit_graph_954.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_47.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_157.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_47.svg -> ../html-full/inherit_graph_157.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_211.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_987.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_211.svg -> ../html-full/inherit_graph_987.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_200.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_956.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_200.svg -> ../html-full/inherit_graph_956.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_223.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1033.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_223.svg -> ../html-full/inherit_graph_1033.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_198.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_951.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_198.svg -> ../html-full/inherit_graph_951.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_22.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_86.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_22.svg -> ../html-full/inherit_graph_86.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_175.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_756.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_175.svg -> ../html-full/inherit_graph_756.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_18.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_75.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_18.svg -> ../html-full/inherit_graph_75.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_160.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_675.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_160.svg -> ../html-full/inherit_graph_675.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_217.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1005.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_217.svg -> ../html-full/inherit_graph_1005.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_227.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1046.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_227.svg -> ../html-full/inherit_graph_1046.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_88.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_352.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_88.svg -> ../html-full/inherit_graph_352.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_171.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_722.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_171.svg -> ../html-full/inherit_graph_722.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_228.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1057.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_228.svg -> ../html-full/inherit_graph_1057.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_90.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_353.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_90.svg -> ../html-full/inherit_graph_353.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_105.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_426.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_105.svg -> ../html-full/inherit_graph_426.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_71.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_250.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_71.svg -> ../html-full/inherit_graph_250.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_212.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_989.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_212.svg -> ../html-full/inherit_graph_989.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_167.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_701.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_167.svg -> ../html-full/inherit_graph_701.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_165.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_692.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_165.svg -> ../html-full/inherit_graph_692.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_158.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_662.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_158.svg -> ../html-full/inherit_graph_662.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_62.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_224.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_62.svg -> ../html-full/inherit_graph_224.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_157.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_661.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_157.svg -> ../html-full/inherit_graph_661.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_159.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_664.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_159.svg -> ../html-full/inherit_graph_664.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_196.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_512.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_196.svg -> ../html-lib/inherit_graph_512.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_122.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_500.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_122.svg -> ../html-full/inherit_graph_500.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_181.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_768.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_181.svg -> ../html-full/inherit_graph_768.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_35.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_6.svg -> ../html-full/inherit_graph_35.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_180.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_767.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_180.svg -> ../html-full/inherit_graph_767.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_13.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_53.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_13.svg -> ../html-full/inherit_graph_53.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_179.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_766.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_179.svg -> ../html-full/inherit_graph_766.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_225.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1035.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_225.svg -> ../html-full/inherit_graph_1035.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_166.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_693.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_166.svg -> ../html-full/inherit_graph_693.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_25.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_4.svg -> ../html-full/inherit_graph_25.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_150.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_649.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_150.svg -> ../html-full/inherit_graph_649.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_102.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_423.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_102.svg -> ../html-full/inherit_graph_423.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_193.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_940.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_193.svg -> ../html-full/inherit_graph_940.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_25.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_103.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_25.svg -> ../html-full/inherit_graph_103.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_213.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_992.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_213.svg -> ../html-full/inherit_graph_992.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_188.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_919.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_188.svg -> ../html-full/inherit_graph_919.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_10.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_50.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_10.svg -> ../html-full/inherit_graph_50.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_20.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_82.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_20.svg -> ../html-full/inherit_graph_82.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_164.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_691.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_164.svg -> ../html-full/inherit_graph_691.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_104.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_425.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_104.svg -> ../html-full/inherit_graph_425.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_177.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_761.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_177.svg -> ../html-full/inherit_graph_761.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_60.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_217.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_60.svg -> ../html-full/inherit_graph_217.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_19.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_76.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_19.svg -> ../html-full/inherit_graph_76.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_186.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_908.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_186.svg -> ../html-full/inherit_graph_908.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_207.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_976.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_207.svg -> ../html-full/inherit_graph_976.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_56.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_180.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_56.svg -> ../html-full/inherit_graph_180.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_145.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_609.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_145.svg -> ../html-full/inherit_graph_609.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_214.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1001.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_214.svg -> ../html-full/inherit_graph_1001.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_141.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_599.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_141.svg -> ../html-full/inherit_graph_599.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_113.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_472.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_113.svg -> ../html-full/inherit_graph_472.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_114.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_483.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_114.svg -> ../html-full/inherit_graph_483.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_131.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_527.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_131.svg -> ../html-full/inherit_graph_527.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_247.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1123.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_247.svg -> ../html-full/inherit_graph_1123.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_58.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_192.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_58.svg -> ../html-full/inherit_graph_192.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_178.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_762.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_178.svg -> ../html-full/inherit_graph_762.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_120.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_493.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_120.svg -> ../html-full/inherit_graph_493.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_100.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_394.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_100.svg -> ../html-full/inherit_graph_394.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_168.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_702.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_168.svg -> ../html-full/inherit_graph_702.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_133.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_571.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_133.svg -> ../html-full/inherit_graph_571.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_246.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1115.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_246.svg -> ../html-full/inherit_graph_1115.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_143.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_601.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_143.svg -> ../html-full/inherit_graph_601.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_137.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_595.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_137.svg -> ../html-full/inherit_graph_595.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_138.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_596.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_138.svg -> ../html-full/inherit_graph_596.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_216.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1003.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_216.svg -> ../html-full/inherit_graph_1003.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_194.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_942.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_194.svg -> ../html-full/inherit_graph_942.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_232.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1088.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_232.svg -> ../html-full/inherit_graph_1088.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_64.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_232.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_64.svg -> ../html-full/inherit_graph_232.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_215.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1002.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_215.svg -> ../html-full/inherit_graph_1002.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_139.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_597.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_139.svg -> ../html-full/inherit_graph_597.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_70.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_249.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_70.svg -> ../html-full/inherit_graph_249.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_187.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_918.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_187.svg -> ../html-full/inherit_graph_918.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_72.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_251.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_72.svg -> ../html-full/inherit_graph_251.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_208.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_977.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_208.svg -> ../html-full/inherit_graph_977.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_222.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1032.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_222.svg -> ../html-full/inherit_graph_1032.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_230.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1060.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_230.svg -> ../html-full/inherit_graph_1060.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_55.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_179.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_55.svg -> ../html-full/inherit_graph_179.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_170.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_707.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_170.svg -> ../html-full/inherit_graph_707.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_132.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_556.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_132.svg -> ../html-full/inherit_graph_556.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_151.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_650.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_151.svg -> ../html-full/inherit_graph_650.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_12.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_52.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_12.svg -> ../html-full/inherit_graph_52.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_245.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1114.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_245.svg -> ../html-full/inherit_graph_1114.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_176.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_760.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_176.svg -> ../html-full/inherit_graph_760.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_101.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_417.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_101.svg -> ../html-full/inherit_graph_417.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_237.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1099.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_237.svg -> ../html-full/inherit_graph_1099.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_219.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1029.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_219.svg -> ../html-full/inherit_graph_1029.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_238.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1102.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_238.svg -> ../html-full/inherit_graph_1102.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_0.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_19.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_0.svg -> ../html-full/inherit_graph_19.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_20.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_1.svg -> ../html-full/inherit_graph_20.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_124.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_514.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_124.svg -> ../html-full/inherit_graph_514.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_142.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_600.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_142.svg -> ../html-full/inherit_graph_600.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_65.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_233.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_65.svg -> ../html-full/inherit_graph_233.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_239.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1103.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_239.svg -> ../html-full/inherit_graph_1103.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_243.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1112.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_243.svg -> ../html-full/inherit_graph_1112.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_252.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1130.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_252.svg -> ../html-full/inherit_graph_1130.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_5.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_27.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_5.svg -> ../html-full/inherit_graph_27.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_233.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1089.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_233.svg -> ../html-full/inherit_graph_1089.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_234.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1090.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_234.svg -> ../html-full/inherit_graph_1090.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_241.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1110.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_241.svg -> ../html-full/inherit_graph_1110.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_169.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_706.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_169.svg -> ../html-full/inherit_graph_706.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_255.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1152.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_255.svg -> ../html-full/inherit_graph_1152.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_173.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_440.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_173.svg -> ../html-lib/inherit_graph_440.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_221.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1031.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_221.svg -> ../html-full/inherit_graph_1031.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_7.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_42.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_7.svg -> ../html-full/inherit_graph_42.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_206.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_974.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_206.svg -> ../html-full/inherit_graph_974.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_257.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1154.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_257.svg -> ../html-full/inherit_graph_1154.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_123.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_501.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_123.svg -> ../html-full/inherit_graph_501.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_161.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_678.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_161.svg -> ../html-full/inherit_graph_678.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_251.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1128.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_251.svg -> ../html-full/inherit_graph_1128.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_156.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_660.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_156.svg -> ../html-full/inherit_graph_660.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_218.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1018.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_218.svg -> ../html-full/inherit_graph_1018.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_220.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1030.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_220.svg -> ../html-full/inherit_graph_1030.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_229.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1059.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_229.svg -> ../html-full/inherit_graph_1059.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_210.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_985.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_210.svg -> ../html-full/inherit_graph_985.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_23.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_2.svg -> ../html-full/inherit_graph_23.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_236.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1097.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_236.svg -> ../html-full/inherit_graph_1097.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_244.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1113.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_244.svg -> ../html-full/inherit_graph_1113.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_256.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1153.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_256.svg -> ../html-full/inherit_graph_1153.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_224.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1034.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_224.svg -> ../html-full/inherit_graph_1034.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_240.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1108.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_240.svg -> ../html-full/inherit_graph_1108.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_231.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1075.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_231.svg -> ../html-full/inherit_graph_1075.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_30.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_49.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_30.svg -> ../html-lib/inherit_graph_49.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_52.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_176.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_52.svg -> ../html-full/inherit_graph_176.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_54.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_178.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_54.svg -> ../html-full/inherit_graph_178.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_250.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1127.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_250.svg -> ../html-full/inherit_graph_1127.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_51.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_165.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_51.svg -> ../html-full/inherit_graph_165.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_242.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1111.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_242.svg -> ../html-full/inherit_graph_1111.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_48.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_158.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_48.svg -> ../html-full/inherit_graph_158.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_248.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1124.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_248.svg -> ../html-full/inherit_graph_1124.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_45.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_155.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_45.svg -> ../html-full/inherit_graph_155.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_53.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_177.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_53.svg -> ../html-full/inherit_graph_177.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_8.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_48.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_8.svg -> ../html-full/inherit_graph_48.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_130.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_526.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_130.svg -> ../html-full/inherit_graph_526.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_249.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1125.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_249.svg -> ../html-full/inherit_graph_1125.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_43.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_152.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_43.svg -> ../html-full/inherit_graph_152.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_24.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_3.svg -> ../html-full/inherit_graph_24.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_46.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_156.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_46.svg -> ../html-full/inherit_graph_156.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_226.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1041.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_226.svg -> ../html-full/inherit_graph_1041.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_9.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_49.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_9.svg -> ../html-full/inherit_graph_49.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_253.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1133.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_253.svg -> ../html-full/inherit_graph_1133.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_254.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1138.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_254.svg -> ../html-full/inherit_graph_1138.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_163.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_690.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_163.svg -> ../html-full/inherit_graph_690.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_209.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_984.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_209.svg -> ../html-full/inherit_graph_984.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21_dark.png -> ../html-full/form_34_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_21.png -> ../html-full/form_34.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/sync_off.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sync_off.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/sync_off.png -> ../html-full/sync_off.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/sync_on.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sync_on.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/sync_on.png -> ../html-full/sync_on.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plusd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plusd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plusd.svg -> ../html-full/plusd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plus.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plus.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/plus.svg -> ../html-full/plus.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_8_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_8_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_8_dark.png -> ../html-full/form_8_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bc_s.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bc_s.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bc_s.png -> ../html-full/bc_s.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_8.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_8.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_8.png -> ../html-full/form_8.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bc_sd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bc_sd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/bc_sd.png -> ../html-full/bc_sd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/minusd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/minusd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/minusd.svg -> ../html-full/minusd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/minus.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/minus.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/minus.svg -> ../html-full/minus.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_9_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9_dark.png -> ../html-full/form_9_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_17_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_30_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_17_dark.png -> ../html-full/form_30_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_9.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_9.png -> ../html-full/form_9.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_7_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_7_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_7_dark.png -> ../html-full/form_7_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_17.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_30.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_17.png -> ../html-full/form_30.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_28_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_58_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_28_dark.png -> ../html-full/form_58_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_7.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_7.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_7.png -> ../html-full/form_7.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_19_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_32_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_19_dark.png -> ../html-full/form_32_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_28.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_58.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_28.png -> ../html-full/form_58.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_19.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_32.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_19.png -> ../html-full/form_32.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/splitbar.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/splitbar.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/splitbar.png -> ../html-full/splitbar.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/splitbard.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/splitbard.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/splitbard.png -> ../html-full/splitbard.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_sd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_sd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_sd.png -> ../html-full/tab_sd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_s.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_s.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_s.png -> ../html-full/tab_s.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_hd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_hd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_hd.png -> ../html-full/tab_hd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_h.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_h.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_h.png -> ../html-full/tab_h.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_bd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_bd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_bd.png -> ../html-full/tab_bd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_fd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_fd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_fd.png -> ../html-full/nav_fd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_b.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_b.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_b.png -> ../html-full/tab_b.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_f.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_f.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_f.png -> ../html-full/nav_f.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_a.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_a.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_a.png -> ../html-full/tab_a.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_ad.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_ad.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tab_ad.png -> ../html-full/tab_ad.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/closed.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/closed.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/closed.png -> ../html-full/closed.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/open.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/open.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/open.png -> ../html-full/open.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_hd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_hd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_hd.png -> ../html-full/nav_hd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_h.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_h.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_h.png -> ../html-full/nav_h.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_g.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_g.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/nav_g.png -> ../html-full/nav_g.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.js -> ../../html-full/search/search.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/search.css -> ../../html-full/search/search.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1d.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1b.js -> all_1d.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_c.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_c.js -> ../../html-lib/search/enums_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_sel.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_sel.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_sel.svg -> ../../html-full/search/mag_sel.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_seld.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_seld.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_seld.svg -> ../../html-full/search/mag_seld.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_4.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_4.js -> ../../html-full/search/pages_5.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/close.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/close.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/close.svg -> ../../html-full/search/close.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_9.js -> ../../html-lib/search/defines_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_11.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_11.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_11.js -> ../../html-lib/search/enumvalues_11.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag.svg -> ../../html-full/search/mag.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_d.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_d.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/mag_d.svg -> ../../html-full/search/mag_d.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_13.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_13.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_13.js -> ../../html-lib/search/enumvalues_13.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_a.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_a.js -> ../../html-lib/search/functions_a.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_14.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_14.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_14.js -> ../../html-lib/search/enumvalues_14.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1c.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/all_1c.js -> ../../html-lib/search/all_1c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/functions_1a.js -> ../../html-lib/search/all_1c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/variables_a.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_a.js -> ../../html-lib/search/variables_a.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_3.js -> ../../html-full/search/pages_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_7.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_7.js -> ../../html-lib/search/defines_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_9.js -> ../../html-lib/search/enums_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/variables_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/variables_9.js -> ../../html-lib/search/variables_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_4.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_4.js -> ../../html-lib/search/defines_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> ../../html-full/search/enums_13.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_1.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> ../../html-lib/search/related_1.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/classes_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/classes_9.js -> ../../html-lib/search/classes_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_9.js -> ../../html-full/search/pages_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_0.js -> ../../html-full/search/defines_0.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enumvalues_9.js -> ../../html-lib/search/enumvalues_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_13.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_13.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_13.js -> ../../html-lib/search/typedefs_13.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_d.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_a.js -> ../../html-lib/search/defines_d.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_11.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_f.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_f.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_f.js -> ../../html-full/search/enums_f.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_15.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_15.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_15.js -> ../../html-full/search/enums_15.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_6.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/defines_6.js -> ../../html-lib/search/defines_6.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/jquery.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/jquery.js -> ../html-full/jquery.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_module-deps.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_module-deps.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_module-deps.svg -> ../html-full/dot_module-deps.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tests_2outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tests_2outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tests_2outputadapters_8h__incl.svg -> ../html-full/tests_2outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniont__iparams.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniont__iparams.xhtml -> ../html-full/uniont__iparams.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/quadraticsplinetable_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/quadraticsplinetable_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/quadraticsplinetable_8h__incl.svg -> ../html-full/quadraticsplinetable_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cubicsplinetable_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cubicsplinetable_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cubicsplinetable_8h__incl.svg -> ../html-full/cubicsplinetable_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tests_2requirements_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tests_2requirements_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tests_2requirements_8h__incl.svg -> ../html-full/tests_2requirements_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/template_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinate__test_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/coordinate__test_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinate__test_8h__incl.svg -> ../html-full/coordinate__test_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__math_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simd__math_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__math_8h__incl.svg -> ../html-full/simd__math_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbc__simd_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pbc__simd_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbc__simd_8h__incl.svg -> ../html-full/pbc__simd_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vector__operations_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/vector__operations_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vector__operations_8h__incl.svg -> ../html-full/vector__operations_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/include_2gromacs_2simd_2simd_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/include_2gromacs_2simd_2simd_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/include_2gromacs_2simd_2simd_8h__incl.svg -> ../html-full/include_2gromacs_2simd_2simd_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hsimd__declarations_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hsimd__declarations_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hsimd__declarations_8h__incl.svg -> ../html-full/hsimd__declarations_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule__impl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/restraintmdmodule__impl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule__impl_8h__incl.svg -> ../html-full/restraintmdmodule__impl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationinput_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationinput_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationinput_8h__incl.svg -> ../html-full/simulationinput_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__libraryapi.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__libraryapi.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__libraryapi.svg -> ../html-full/group__group__libraryapi.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__sycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h__incl.svg -> ../html-full/gpuregiontimer__sycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1basic__mdspan.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1basic__mdspan.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1basic__mdspan.xhtml -> ../html-full/classgmx_1_1basic__mdspan.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ocl__compiler_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ocl__compiler_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ocl__compiler_8h__incl.svg -> ../html-full/ocl__compiler_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nbnxm__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm__gpu_8h__incl.svg -> ../html-full/nbnxm__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__sycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/devicebuffer__sycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__sycl_8h__incl.svg -> ../html-full/devicebuffer__sycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__ocl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/devicebuffer__ocl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__ocl_8h__incl.svg -> ../html-full/devicebuffer__ocl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputadapters_8h__incl.svg -> ../html-full/outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atomdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/atomdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atomdata_8h__incl.svg -> ../html-full/atomdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__types__host_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__gpu__types__host_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__types__host_8h__incl.svg -> ../html-full/pme__gpu__types__host_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec__struct_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/domdec__struct_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec__struct_8h__incl.svg -> ../html-full/domdec__struct_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/leapfrog__gpu__internal_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/leapfrog__gpu__internal_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/leapfrog__gpu__internal_8h__incl.svg -> ../html-full/leapfrog__gpu__internal_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/leapfrog__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/leapfrog__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/leapfrog__gpu_8h__incl.svg -> ../html-full/leapfrog__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nvshmem__utils_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8cpp__incl.svg -> ../html-full/nvshmem__utils_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_modularsimulator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_modularsimulator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_modularsimulator.xhtml -> ../html-full/page_modularsimulator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doxygen.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doxygen.css -> ../html-full/doxygen.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__ocl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__ocl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__ocl_8h__incl.svg -> ../html-full/gpuregiontimer__ocl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/runner_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/runner_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/runner_8h__incl.svg -> ../html-full/runner_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__ocl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__ocl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__ocl_8h__incl.svg -> ../html-full/device__event__ocl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference_8h__incl.svg -> ../html-full/impl__reference_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/state_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/state_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/state_8h__incl.svg -> ../html-full/state_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/checkpointdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/checkpointdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/checkpointdata_8h__incl.svg -> ../html-full/checkpointdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/oclutils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/oclutils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/oclutils_8h__incl.svg -> ../html-full/oclutils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lincs__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lincs__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lincs__gpu_8h__incl.svg -> ../html-full/lincs__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionstoragetemplate_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionstoragetemplate_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionstoragetemplate_8h__incl.svg -> ../html-full/optionstoragetemplate_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_simd.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_simd.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_simd.xhtml -> ../html-full/page_simd.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PaddedVector.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PaddedVector.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PaddedVector.xhtml -> ../html-full/classgmx_1_1PaddedVector.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__pp__comm__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__pp__comm__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__pp__comm__gpu_8h__incl.svg -> ../html-full/pme__pp__comm__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniont__iparams-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniont__iparams-members.xhtml -> ../html-full/uniont__iparams-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MultiDimArray.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MultiDimArray.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MultiDimArray.xhtml -> ../html-full/classgmx_1_1MultiDimArray.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FixedCapacityVector.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FixedCapacityVector.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FixedCapacityVector.xhtml -> ../html-full/classgmx_1_1FixedCapacityVector.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forcebuffers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/forcebuffers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forcebuffers_8h__incl.svg -> ../html-full/forcebuffers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boxmatrix_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/boxmatrix_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boxmatrix_8h__incl.svg -> ../html-full/boxmatrix_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__staging_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__gpu__staging_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__staging_8h__incl.svg -> ../html-full/pme__gpu__staging_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__hip_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/devicebuffer__hip_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__hip_8h__incl.svg -> ../html-full/devicebuffer__hip_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifiers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdmodulesnotifiers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifiers_8h__incl.svg -> ../html-full/mdmodulesnotifiers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hostallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hostallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hostallocator_8h__incl.svg -> ../html-full/hostallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/naming_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/naming_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/naming_8h__incl.svg -> ../html-full/naming_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/reversetopology_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/reversetopology_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/reversetopology_8h__incl.svg -> ../html-full/reversetopology_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_97821878ed085dbd2f2120a3dfffc97e_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_97821878ed085dbd2f2120a3dfffc97e_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_97821878ed085dbd2f2120a3dfffc97e_dep.svg -> ../html-full/dir_97821878ed085dbd2f2120a3dfffc97e_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__oriresdata.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata.xhtml -> ../html-full/structt__oriresdata.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gammadistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gammadistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gammadistribution_8h__incl.svg -> ../html-full/gammadistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils__hip_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpu__utils__hip_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils__hip_8cpp__incl.svg -> ../html-full/gpu__utils__hip_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__data__mgmt_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpu__data__mgmt_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__data__mgmt_8h__incl.svg -> ../html-full/gpu__data__mgmt_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputselector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputselector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputselector_8h__incl.svg -> ../html-full/outputselector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BasicVector.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BasicVector.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BasicVector.xhtml -> ../html-full/classgmx_1_1BasicVector.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestReferenceChecker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestReferenceChecker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestReferenceChecker-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestReferenceChecker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nrjac_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8cpp__incl.svg -> ../html-full/nrjac_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nbnxm_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm_8h__incl.svg -> ../html-full/nbnxm_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mrcdensitymapheader_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mrcdensitymapheader_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mrcdensitymapheader_8h__incl.svg -> ../html-full/mrcdensitymapheader_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/updategroupscog_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/updategroupscog_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/updategroupscog_8h__incl.svg -> ../html-full/updategroupscog_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boxdeformation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/boxdeformation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/boxdeformation_8h__incl.svg -> ../html-full/boxdeformation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__util__double_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__util__double_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__util__double_8h__incl.svg -> ../html-full/impl__reference__util__double_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForeignLambdaTerms.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForeignLambdaTerms.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForeignLambdaTerms.xhtml -> ../html-full/classForeignLambdaTerms.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000051_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000051_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000051_000002.xhtml -> ../html-full/dir_000051_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1extents.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1extents.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1extents.xhtml -> ../html-full/classgmx_1_1extents.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution.xhtml -> ../html-full/classgmx_1_1NormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bench__system_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bench__system_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bench__system_8h__incl.svg -> ../html-full/bench__system_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/repeatingsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/repeatingsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/repeatingsection_8h__incl.svg -> ../html-full/repeatingsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right_1_1mapping.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1layout__right_1_1mapping.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right_1_1mapping.xhtml -> ../html-full/classgmx_1_1layout__right_1_1mapping.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/basicoptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/basicoptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/basicoptions_8h__incl.svg -> ../html-full/basicoptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9819c9c4470e480e08d3e56c84b45715_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9819c9c4470e480e08d3e56c84b45715_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9819c9c4470e480e08d3e56c84b45715_dep.svg -> ../html-full/dir_9819c9c4470e480e08d3e56c84b45715_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoption_8h__incl.svg -> ../html-full/selectionoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/legacymdrunoptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/legacymdrunoptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/legacymdrunoptions_8h__incl.svg -> ../html-full/legacymdrunoptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/densityfittingforce_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/densityfittingforce_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/densityfittingforce_8h__incl.svg -> ../html-full/densityfittingforce_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/update__constrain__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/update__constrain__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/update__constrain__gpu_8h__incl.svg -> ../html-full/update__constrain__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_830dfad27752fb63c14945fb48d9c41a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_830dfad27752fb63c14945fb48d9c41a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_830dfad27752fb63c14945fb48d9c41a_dep.svg -> ../html-full/dir_830dfad27752fb63c14945fb48d9c41a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectioncollection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectioncollection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectioncollection_8h__incl.svg -> ../html-full/selectioncollection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000037_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000037_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000037_000002.xhtml -> ../html-full/dir_000037_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datatest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/datatest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datatest_8h__incl.svg -> ../html-full/datatest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectBuilder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeObjectBuilder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectBuilder.xhtml -> ../html-full/classgmx_1_1KeyValueTreeObjectBuilder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinerunner_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinerunner_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinerunner_8h__incl.svg -> ../html-full/cmdlinerunner_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/invertmatrix_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/invertmatrix_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/invertmatrix_8h__incl.svg -> ../html-full/invertmatrix_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple-members.xhtml -> ../html-full/classgmx_1_1OptionStorageTemplateSimple-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd__double_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__simd__double_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd__double_8h__incl.svg -> ../html-full/impl__reference__simd__double_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ListOfLists.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ListOfLists.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ListOfLists.xhtml -> ../html-full/classgmx_1_1ListOfLists.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8ba78a6afd206a530db53d1b86459b20_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8ba78a6afd206a530db53d1b86459b20_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8ba78a6afd206a530db53d1b86459b20_dep.svg -> ../html-full/dir_8ba78a6afd206a530db53d1b86459b20_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/average_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/average_8h__incl.svg -> ../html-full/average_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataAverageModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataBinAverageModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/frameconverter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverter_8h__incl.svg -> ../html-full/frameconverter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mrcdensitymap_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mrcdensitymap_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mrcdensitymap_8h__incl.svg -> ../html-full/mrcdensitymap_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/wholemoleculetransform_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/wholemoleculetransform_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/wholemoleculetransform_8h__incl.svg -> ../html-full/wholemoleculetransform_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gausstransform_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gausstransform_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gausstransform_8h__incl.svg -> ../html-full/gausstransform_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/histogram_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/histogram_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/histogram_8h__incl.svg -> ../html-full/histogram_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_17.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_17.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_17.svg -> ../html-full/msc_inline_mscgraph_17.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_11.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_11.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_11.svg -> ../html-full/msc_inline_mscgraph_11.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structCheckpointHeaderContents.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structCheckpointHeaderContents.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structCheckpointHeaderContents.xhtml -> ../html-full/structCheckpointHeaderContents.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataLifetimeModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationWorkload.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationWorkload.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationWorkload.xhtml -> ../html-full/classgmx_1_1SimulationWorkload.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinatefile_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/coordinatefile_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinatefile_8h__incl.svg -> ../html-full/coordinatefile_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c0cf0fe0f6109acd05f931add0b1fc8d_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c0cf0fe0f6109acd05f931add0b1fc8d_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c0cf0fe0f6109acd05f931add0b1fc8d_dep.svg -> ../html-full/dir_c0cf0fe0f6109acd05f931add0b1fc8d_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnumerationArray.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnumerationArray.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnumerationArray.xhtml -> ../html-full/structgmx_1_1EnumerationArray.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lifetime_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lifetime_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lifetime_8h__incl.svg -> ../html-full/lifetime_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threefry_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/threefry_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threefry_8h__incl.svg -> ../html-full/threefry_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg -> ../html-full/api_2legacy_2include_2gromacs_2trajectoryanalysis_2analysismodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinatetransformation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/coordinatetransformation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coordinatetransformation_8h__incl.svg -> ../html-full/coordinatetransformation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/paddedvector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/paddedvector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/paddedvector_8h__incl.svg -> ../html-full/paddedvector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gromacs_2mdrunutility_2freeenergy_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gromacs_2mdrunutility_2freeenergy_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gromacs_2mdrunutility_2freeenergy_8cpp__incl.svg -> ../html-full/gromacs_2mdrunutility_2freeenergy_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classSimulationParticle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classSimulationParticle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classSimulationParticle.xhtml -> ../html-full/classSimulationParticle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__information_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__information_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__information_8h__incl.svg -> ../html-full/device__information_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000171_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000002.xhtml -> ../html-full/dir_000171_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1H5md.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1H5md.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1H5md.xhtml -> ../html-full/classgmx_1_1H5md.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataValue.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataValue.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataValue.xhtml -> ../html-full/classgmx_1_1AnalysisDataValue.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplate-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplate-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplate-members.xhtml -> ../html-full/classgmx_1_1OptionStorageTemplate-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroupsCog.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UpdateGroupsCog.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroupsCog.xhtml -> ../html-full/classgmx_1_1UpdateGroupsCog.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listoflists_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/listoflists_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listoflists_8h__incl.svg -> ../html-full/listoflists_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_de13c8102fdf6675feef765f04939cef_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_de13c8102fdf6675feef765f04939cef_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_de13c8102fdf6675feef765f04939cef_dep.svg -> ../html-full/dir_de13c8102fdf6675feef765f04939cef_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption-members.xhtml -> ../html-full/classgmx_1_1FileNameOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__sycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__sycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__sycl_8h__incl.svg -> ../html-full/device__event__sycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/conftest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/conftest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/conftest_8h__incl.svg -> ../html-full/conftest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/xvgtest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/xvgtest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/xvgtest_8h__incl.svg -> ../html-full/xvgtest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__utility.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__utility.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__utility.svg -> ../html-full/group__module__utility.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram-members.xhtml -> ../html-full/classgmx_1_1AbstractAverageHistogram-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mock__datamodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mock__datamodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mock__datamodule_8h__incl.svg -> ../html-full/mock__datamodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/real_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/real_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/real_8h.xhtml -> ../html-full/real_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuhaloexchange_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuhaloexchange_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuhaloexchange_8h__incl.svg -> ../html-full/gpuhaloexchange_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/math_2include_2gromacs_2math_2matrix_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/math_2include_2gromacs_2math_2matrix_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/math_2include_2gromacs_2math_2matrix_8h__incl.svg -> ../html-full/math_2include_2gromacs_2math_2matrix_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyoutput_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/energyoutput_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyoutput_8h__incl.svg -> ../html-full/energyoutput_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1basic__mdspan-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1basic__mdspan-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1basic__mdspan-members.xhtml -> ../html-full/classgmx_1_1basic__mdspan-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PaddedVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PaddedVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PaddedVector-members.xhtml -> ../html-full/classgmx_1_1PaddedVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/strconvert_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/strconvert_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/strconvert_8h__incl.svg -> ../html-full/strconvert_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringtoenumvalueconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringtoenumvalueconverter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringtoenumvalueconverter_8h__incl.svg -> ../html-full/stringtoenumvalueconverter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datastorage_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/datastorage_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datastorage_8h__incl.svg -> ../html-full/datastorage_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption-members.xhtml -> ../html-full/classgmx_1_1SelectionOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arraydata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arraydata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arraydata_8h__incl.svg -> ../html-full/arraydata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selection_8h__incl.svg -> ../html-full/selection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_18.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_18.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_18.svg -> ../html-full/msc_inline_mscgraph_18.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StepWorkload.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StepWorkload.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StepWorkload.xhtml -> ../html-full/classgmx_1_1StepWorkload.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/valueconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/valueconverter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/valueconverter_8h__incl.svg -> ../html-full/valueconverter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_991d69cdcf3b0071ea60d8f00677bf1a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_991d69cdcf3b0071ea60d8f00677bf1a_dep.svg -> ../html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pull_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull_8h__incl.svg -> ../html-full/pull_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000055_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000055_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000055_000052.xhtml -> ../html-full/dir_000055_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000056_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000056_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000056_000052.xhtml -> ../html-full/dir_000056_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPositions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPositions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPositions.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPositions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialmovingaverage_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/exponentialmovingaverage_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialmovingaverage_8h__incl.svg -> ../html-full/exponentialmovingaverage_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataVectorPlotModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nonbonded__verlet__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nonbonded__verlet__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nonbonded__verlet__t-members.xhtml -> ../html-full/structgmx_1_1nonbonded__verlet__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__context_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__context_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__context_8h__incl.svg -> ../html-full/device__context_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inmemoryserializer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inmemoryserializer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inmemoryserializer_8h__incl.svg -> ../html-full/inmemoryserializer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationcontext_8h__incl.svg -> ../html-full/simulationcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption-members.xhtml -> ../html-full/classgmx_1_1LegacyEnumOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputadaptercontainer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadaptercontainer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputadaptercontainer_8h__incl.svg -> ../html-full/outputadaptercontainer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataWeightedHistogramModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_analysisdata.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_analysisdata.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_analysisdata.xhtml -> ../html-full/page_analysisdata.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/makeconstraints_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/makeconstraints_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/makeconstraints_8h__incl.svg -> ../html-full/makeconstraints_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FixedCapacityVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FixedCapacityVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FixedCapacityVector-members.xhtml -> ../html-full/classgmx_1_1FixedCapacityVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataSimpleHistogramModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption-members.xhtml -> ../html-full/classgmx_1_1StringOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ga2la_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ga2la_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ga2la_8h__incl.svg -> ../html-full/ga2la_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_4.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_4.svg -> ../html-full/msc_inline_mscgraph_4.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listed__forces_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/listed__forces_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listed__forces_8h__incl.svg -> ../html-full/listed__forces_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils__hip_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpu__utils__hip_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils__hip_8cpp.xhtml -> ../html-full/gpu__utils__hip_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lincs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lincs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/lincs_8h__incl.svg -> ../html-full/lincs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption-members.xhtml -> ../html-full/classgmx_1_1EnumOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/exponentialdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exponentialdistribution_8h__incl.svg -> ../html-full/exponentialdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_7.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_7.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_7.svg -> ../html-full/msc_inline_mscgraph_7.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption-members.xhtml -> ../html-full/classgmx_1_1DoubleOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/normaldistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/normaldistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/normaldistribution_8h__incl.svg -> ../html-full/normaldistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_29f1a674ba1859f41704372482980b85_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85_dep.svg -> ../html-full/dir_29f1a674ba1859f41704372482980b85_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Allocator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Allocator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Allocator.xhtml -> ../html-full/classgmx_1_1Allocator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption-members.xhtml -> ../html-full/classgmx_1_1FloatOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpueventsynchronizer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer_8h__incl.svg -> ../html-full/gpueventsynchronizer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/locality_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/locality_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/locality_8h__incl.svg -> ../html-full/locality_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GromacsException__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GromacsException__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GromacsException__inherit__graph.svg -> ../html-full/classgmx_1_1GromacsException__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption-members.xhtml -> ../html-full/classgmx_1_1IntegerOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa16baa95be1082e33976e526f10737d_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_fa16baa95be1082e33976e526f10737d_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa16baa95be1082e33976e526f10737d_dep.svg -> ../html-full/dir_fa16baa95be1082e33976e526f10737d_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreebuilder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/keyvaluetreebuilder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreebuilder_8h__incl.svg -> ../html-full/keyvaluetreebuilder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testasserts_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testasserts_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testasserts_8h__incl.svg -> ../html-full/testasserts_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ef8749c40eccc3a09efb31c9845a0752_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ef8749c40eccc3a09efb31c9845a0752_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ef8749c40eccc3a09efb31c9845a0752_dep.svg -> ../html-full/dir_ef8749c40eccc3a09efb31c9845a0752_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreetransform_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/keyvaluetreetransform_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreetransform_8h__incl.svg -> ../html-full/keyvaluetreetransform_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataPlotModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option-members.xhtml -> ../html-full/classgmx_1_1Int64Option-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000002.xhtml -> ../html-full/dir_000111_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/utility_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/utility_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/utility_8h__incl.svg -> ../html-full/utility_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataDisplacementModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg -> ../html-full/dir_852ca012cdae2a5a395a4686bde0b5a5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption-members.xhtml -> ../html-full/classgmx_1_1BooleanOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/template__mp_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template__mp_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/template__mp_8h__incl.svg -> ../html-full/template__mp_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/constr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/constr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/constr_8h__incl.svg -> ../html-full/constr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ifunc_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8cpp.xhtml -> ../html-full/ifunc_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate-members.xhtml -> ../html-full/classgmx_1_1OptionTemplate-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionList.xhtml -> ../html-full/structInteractionList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hashedmap_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hashedmap_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hashedmap_8h__incl.svg -> ../html-full/hashedmap_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/multidimarray_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/multidimarray_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/multidimarray_8h__incl.svg -> ../html-full/multidimarray_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerWrapper.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classGpuRegionTimerWrapper.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerWrapper.xhtml -> ../html-full/classGpuRegionTimerWrapper.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule-members.xhtml -> ../html-full/classgmx_1_1AbstractPlotModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderInput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput.xhtml -> ../html-full/classgmx_1_1ForceProviderInput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/multisim_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/multisim_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/multisim_8h__incl.svg -> ../html-full/multisim_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doxygen.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doxygen.svg -> ../html-full/doxygen.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/compare_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/compare_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/compare_8h.xhtml -> ../html-full/compare_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameAverageModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisArrayData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAnalysisArrayData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisArrayData-members.xhtml -> ../html-full/classgmx_1_1AbstractAnalysisArrayData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionStorage-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionStorage-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionStorage-members.xhtml -> ../html-full/classgmx_1_1AbstractOptionStorage-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a651860364c792068346b3bf7e517a4d_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a651860364c792068346b3bf7e517a4d_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a651860364c792068346b3bf7e517a4d_dep.svg -> ../html-full/dir_a651860364c792068346b3bf7e517a4d_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dataframe_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dataframe_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dataframe_8h__incl.svg -> ../html-full/dataframe_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData-members.xhtml -> ../html-full/classgmx_1_1AnalysisArrayData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_mdmodules.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_mdmodules.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_mdmodules.xhtml -> ../html-full/page_mdmodules.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsection_8h__incl.svg -> ../html-full/optionsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_refdata.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_refdata.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_refdata.xhtml -> ../html-full/page_refdata.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_81cdfb33ccaae5eb79bfee83205e9034_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_81cdfb33ccaae5eb79bfee83205e9034_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_81cdfb33ccaae5eb79bfee83205e9034_dep.svg -> ../html-full/dir_81cdfb33ccaae5eb79bfee83205e9034_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1accessor__basic.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic.xhtml -> ../html-full/classgmx_1_1accessor__basic.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1OutputSelectorDeathTest-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest-members.xhtml -> ../html-full/classgmx_1_1test_1_1OutputSelectorDeathTest-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceWithVirial.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial.xhtml -> ../html-full/classgmx_1_1ForceWithVirial.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classekinstate__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classekinstate__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classekinstate__t.xhtml -> ../html-full/classekinstate__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/syclutils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/syclutils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/syclutils_8h__incl.svg -> ../html-full/syclutils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/resethandler_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/resethandler_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/resethandler_8h__incl.svg -> ../html-full/resethandler_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatch.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculePatch.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatch.xhtml -> ../html-full/structMoleculePatch.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbsearch_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nbsearch_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbsearch_8h__incl.svg -> ../html-full/nbsearch_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDensityMapHeader.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader.xhtml -> ../html-full/structgmx_1_1MrcDensityMapHeader.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabulatednormaldistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tabulatednormaldistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabulatednormaldistribution_8h__incl.svg -> ../html-full/tabulatednormaldistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/settle_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/settle_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/settle_8h__incl.svg -> ../html-full/settle_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pargs.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__pargs.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pargs.xhtml -> ../html-full/structt__pargs.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDDBalanceRegionHandler.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classDDBalanceRegionHandler.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDDBalanceRegionHandler.xhtml -> ../html-full/classDDBalanceRegionHandler.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forceoutput_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/forceoutput_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forceoutput_8h__incl.svg -> ../html-full/forceoutput_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/refdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/refdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/refdata_8h__incl.svg -> ../html-full/refdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BasicVector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BasicVector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BasicVector-members.xhtml -> ../html-full/classgmx_1_1BasicVector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stophandler_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stophandler_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stophandler_8h__incl.svg -> ../html-full/stophandler_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e1ed358ca35c2ff10e9db40fa7a56556_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_e1ed358ca35c2ff10e9db40fa7a56556_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e1ed358ca35c2ff10e9db40fa7a56556_dep.svg -> ../html-full/dir_e1ed358ca35c2ff10e9db40fa7a56556_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/long__range__correction_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/long__range__correction_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/long__range__correction_8h.xhtml -> ../html-full/long__range__correction_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSet.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LocalAtomSet.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSet.xhtml -> ../html-full/classgmx_1_1LocalAtomSet.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter.xhtml -> ../html-full/classgmx_1_1IOutputAdapter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformrealdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniformrealdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformrealdistribution_8h__incl.svg -> ../html-full/uniformrealdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3dfde880c4fe7255f4f58a755a0d4b27.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3dfde880c4fe7255f4f58a755a0d4b27.xhtml -> ../html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1GammaDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Selection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Selection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Selection-members.xhtml -> ../html-full/classgmx_1_1Selection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/int64__to__int_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/int64__to__int_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/int64__to__int_8h__incl.svg -> ../html-full/int64__to__int_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ISerializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ISerializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ISerializer-members.xhtml -> ../html-full/classgmx_1_1ISerializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1NormalDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IEnergyAnalysis.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IEnergyAnalysis.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IEnergyAnalysis.xhtml -> ../html-full/classgmx_1_1IEnergyAnalysis.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7f62cfb443030700e40f19f5b91687f8_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7f62cfb443030700e40f19f5b91687f8_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7f62cfb443030700e40f19f5b91687f8_dep.svg -> ../html-full/dir_7f62cfb443030700e40f19f5b91687f8_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d7a8cfe5a4a9a220f003dbc4ba202e38_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_d7a8cfe5a4a9a220f003dbc4ba202e38_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d7a8cfe5a4a9a220f003dbc4ba202e38_dep.svg -> ../html-full/dir_d7a8cfe5a4a9a220f003dbc4ba202e38_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FlagsTemplate.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FlagsTemplate.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FlagsTemplate.xhtml -> ../html-full/classgmx_1_1FlagsTemplate.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classWarningHandler.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classWarningHandler.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classWarningHandler.xhtml -> ../html-full/classWarningHandler.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event_8h__incl.svg -> ../html-full/device__event_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPair.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPair.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPair.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPair.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5cdafd7241d2493bf10eba16c24df27_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a5cdafd7241d2493bf10eba16c24df27_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5cdafd7241d2493bf10eba16c24df27_dep.svg -> ../html-full/dir_a5cdafd7241d2493bf10eba16c24df27_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_16.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_16.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_16.svg -> ../html-full/msc_inline_mscgraph_16.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/handlerestart_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/handlerestart_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/handlerestart_8h__incl.svg -> ../html-full/handlerestart_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionmanager_8h__incl.svg -> ../html-full/selectionoptionmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoptionmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenameoptionmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoptionmanager_8h__incl.svg -> ../html-full/filenameoptionmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetForceSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles-members.xhtml -> ../html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyGroupsPerCluster.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyGroupsPerCluster.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyGroupsPerCluster.xhtml -> ../html-full/classgmx_1_1EnergyGroupsPerCluster.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoOptionalOutput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput-members.xhtml -> ../html-full/classgmx_1_1test_1_1NoOptionalOutput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MembedHolder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MembedHolder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MembedHolder.xhtml -> ../html-full/classgmx_1_1MembedHolder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractsection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractsection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractsection_8h__incl.svg -> ../html-full/abstractsection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffersView.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceBuffersView.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffersView.xhtml -> ../html-full/classgmx_1_1ForceBuffersView.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WholeMoleculeTransform.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1WholeMoleculeTransform.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WholeMoleculeTransform.xhtml -> ../html-full/classgmx_1_1WholeMoleculeTransform.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setatoms_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setatoms_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setatoms_8h__incl.svg -> ../html-full/setatoms_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mp11_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mp11_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mp11_8h__incl.svg -> ../html-full/mp11_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnumerationArray-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnumerationArray-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnumerationArray-members.xhtml -> ../html-full/structgmx_1_1EnumerationArray-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mock__helptopic_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mock__helptopic_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mock__helptopic_8h__incl.svg -> ../html-full/mock__helptopic_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__management_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management_8h__incl.svg -> ../html-full/device__management_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeInformation.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation.xhtml -> ../html-full/structMoleculeInformation.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayrefwithpadding_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arrayrefwithpadding_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayrefwithpadding_8h__incl.svg -> ../html-full/arrayrefwithpadding_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__params_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/awh__params_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__params_8h__incl.svg -> ../html-full/awh__params_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/taskassignment_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/taskassignment_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/taskassignment_8h__incl.svg -> ../html-full/taskassignment_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ArrayRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ArrayRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ArrayRef-members.xhtml -> ../html-full/classgmx_1_1ArrayRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FlagTest-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest-members.xhtml -> ../html-full/classgmx_1_1test_1_1FlagTest-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleTest-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ModuleTest-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleTest-members.xhtml -> ../html-full/classgmx_1_1test_1_1ModuleTest-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions.xhtml -> ../html-full/classInteractionDefinitions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomdecOptions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomdecOptions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomdecOptions.xhtml -> ../html-full/structgmx_1_1DomdecOptions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreePath.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreePath.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreePath.xhtml -> ../html-full/classgmx_1_1KeyValueTreePath.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/futil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/futil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/futil_8h__incl.svg -> ../html-full/futil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testexceptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testexceptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testexceptions_8h__incl.svg -> ../html-full/testexceptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iforceprovider_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iforceprovider_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iforceprovider_8h__incl.svg -> ../html-full/iforceprovider_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_624186332b690fb09aa040ec7109715b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_624186332b690fb09aa040ec7109715b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_624186332b690fb09aa040ec7109715b_dep.svg -> ../html-full/dir_624186332b690fb09aa040ec7109715b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetree_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/keyvaluetree_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetree_8h__incl.svg -> ../html-full/keyvaluetree_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__nblist.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__nblist.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__nblist.xhtml -> ../html-full/classt__nblist.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_6.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_6.svg -> ../html-full/msc_inline_mscgraph_6.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionValueConverterSimple.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionValueConverterSimple.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionValueConverterSimple.xhtml -> ../html-full/classgmx_1_1OptionValueConverterSimple.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_trajectoryanalysisframework.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_trajectoryanalysisframework.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_trajectoryanalysisframework.xhtml -> ../html-full/page_trajectoryanalysisframework.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__options.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__options.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__options.svg -> ../html-full/group__module__options.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution_1_1param__type.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithShiftForces.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceWithShiftForces.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithShiftForces.xhtml -> ../html-full/classgmx_1_1ForceWithShiftForces.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__oriresdata-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata-members.xhtml -> ../html-full/structt__oriresdata-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7d5778d5a7f747f3892a6db000ed3296_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7d5778d5a7f747f3892a6db000ed3296_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7d5778d5a7f747f3892a6db000ed3296_dep.svg -> ../html-full/dir_7d5778d5a7f747f3892a6db000ed3296_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef.xhtml -> ../html-full/structt__idef.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structTpxFileHeader.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structTpxFileHeader.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structTpxFileHeader.xhtml -> ../html-full/structTpxFileHeader.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MappedUnionFinder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder.xhtml -> ../html-full/classgmx_1_1MappedUnionFinder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo-members.xhtml -> ../html-full/classgmx_1_1FileNameOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__analysisdata.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__analysisdata.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__analysisdata.svg -> ../html-full/group__module__analysisdata.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorStateData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulatorStateData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorStateData__coll__graph.svg -> ../html-full/structgmx_1_1SimulatorStateData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPdbAtomEntry.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPdbAtomEntry.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPdbAtomEntry.xhtml -> ../html-full/classPdbAtomEntry.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/requirements_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/requirements_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/requirements_8h__incl.svg -> ../html-full/requirements_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformintdistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniformintdistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/uniformintdistribution_8h__incl.svg -> ../html-full/uniformintdistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/densityfit_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/densityfit_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/densityfit_8h__incl.svg -> ../html-full/densityfit_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__mdrun.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__mdrun.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__mdrun.svg -> ../html-full/group__group__mdrun.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__state-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__state-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__state-members.xhtml -> ../html-full/classt__state-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_15.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_15.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_15.svg -> ../html-full/msc_inline_mscgraph_15.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/resourcedivision_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/resourcedivision_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/resourcedivision_8h__incl.svg -> ../html-full/resourcedivision_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nvshmem__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8h__incl.svg -> ../html-full/nvshmem__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeSolve.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPmeSolve.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeSolve.xhtml -> ../html-full/classPmeSolve.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinetest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinetest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinetest_8h__incl.svg -> ../html-full/cmdlinetest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDLogger.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger.xhtml -> ../html-full/classgmx_1_1MDLogger.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1Range_1_1iterator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Range_1_1iterator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1Range_1_1iterator.xhtml -> ../html-full/structgmx_1_1Range_1_1iterator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/autocorr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/autocorr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/autocorr_8h__incl.svg -> ../html-full/autocorr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ModuleSelection.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection.xhtml -> ../html-full/classgmx_1_1test_1_1ModuleSelection.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1shakedata.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1shakedata.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1shakedata.xhtml -> ../html-full/structgmx_1_1shakedata.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLineTestBase-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineTestBase-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLineTestBase-members.xhtml -> ../html-full/classgmx_1_1test_1_1CommandLineTestBase-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdSetZeroProxy.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdSetZeroProxy.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdSetZeroProxy.xhtml -> ../html-full/classgmx_1_1SimdSetZeroProxy.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/unionfind_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/unionfind_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/unionfind_8h__incl.svg -> ../html-full/unionfind_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPreprocessResidue.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue.xhtml -> ../html-full/structPreprocessResidue.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exceptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/exceptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/exceptions_8h__incl.svg -> ../html-full/exceptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classSimulationParticle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classSimulationParticle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classSimulationParticle-members.xhtml -> ../html-full/classSimulationParticle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayref_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arrayref_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayref_8h.xhtml -> ../html-full/arrayref_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg -> ../html-full/api_2legacy_2include_2gromacs_2options_2options_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hackblock_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hackblock_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hackblock_8h__incl.svg -> ../html-full/hackblock_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structCheckpointHeaderContents-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structCheckpointHeaderContents-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structCheckpointHeaderContents-members.xhtml -> ../html-full/structCheckpointHeaderContents-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fatalerror_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fatalerror_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fatalerror_8h__incl.svg -> ../html-full/fatalerror_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position__restraints_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/position__restraints_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position__restraints_8h__incl.svg -> ../html-full/position__restraints_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ee8b3903a5b832a547d4c24143fdba12_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ee8b3903a5b832a547d4c24143fdba12_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ee8b3903a5b832a547d4c24143fdba12_dep.svg -> ../html-full/dir_ee8b3903a5b832a547d4c24143fdba12_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_19.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_19.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_19.svg -> ../html-full/msc_inline_mscgraph_19.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MultiDimArray-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MultiDimArray-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MultiDimArray-members.xhtml -> ../html-full/classgmx_1_1MultiDimArray-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_10.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_10.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_10.svg -> ../html-full/msc_inline_mscgraph_10.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__mdrun.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__mdrun.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__mdrun.xhtml -> ../html-full/group__group__mdrun.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_07de4f1e1243a01a2bf5cedd79c4a54e_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_07de4f1e1243a01a2bf5cedd79c4a54e_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_07de4f1e1243a01a2bf5cedd79c4a54e_dep.svg -> ../html-full/dir_07de4f1e1243a01a2bf5cedd79c4a54e_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000050_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000050_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000050_000002.xhtml -> ../html-full/dir_000050_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filestream_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filestream_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filestream_8h__incl.svg -> ../html-full/filestream_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationWorkload-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationWorkload-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationWorkload-members.xhtml -> ../html-full/classgmx_1_1SimulationWorkload-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_80b5f348cc1a3cb0c1acdffffc165c01_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_80b5f348cc1a3cb0c1acdffffc165c01_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_80b5f348cc1a3cb0c1acdffffc165c01_dep.svg -> ../html-full/dir_80b5f348cc1a3cb0c1acdffffc165c01_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeValueBuilder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeValueBuilder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeValueBuilder.xhtml -> ../html-full/classgmx_1_1KeyValueTreeValueBuilder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f3f8e47af59009948d5f1b9bd8d0d1fc_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_f3f8e47af59009948d5f1b9bd8d0d1fc_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f3f8e47af59009948d5f1b9bd8d0d1fc_dep.svg -> ../html-full/dir_f3f8e47af59009948d5f1b9bd8d0d1fc_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SelectionTopologyProperties.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SelectionTopologyProperties.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SelectionTopologyProperties.xhtml -> ../html-full/structgmx_1_1SelectionTopologyProperties.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__util__float_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__util__float_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__util__float_8h__incl.svg -> ../html-full/impl__reference__util__float_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__enerdata__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t.xhtml -> ../html-full/structgmx__enerdata__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/include_2gromacs_2utility_2bitmask_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/include_2gromacs_2utility_2bitmask_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/include_2gromacs_2utility_2bitmask_8h__incl.svg -> ../html-full/include_2gromacs_2utility_2bitmask_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData-members.xhtml -> ../html-full/classgmx_1_1AnalysisData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisSettings-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forcetable_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/forcetable_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/forcetable_8h__incl.svg -> ../html-full/forcetable_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_8.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_8.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_8.svg -> ../html-full/msc_inline_mscgraph_8.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OutputRequirements.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OutputRequirements.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OutputRequirements.xhtml -> ../html-full/structgmx_1_1OutputRequirements.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testfileredirector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testfileredirector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testfileredirector_8h__incl.svg -> ../html-full/testfileredirector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyMdrunOptions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyMdrunOptions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyMdrunOptions-members.xhtml -> ../html-full/classgmx_1_1LegacyMdrunOptions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/neldermead_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/neldermead_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/neldermead_8h__incl.svg -> ../html-full/neldermead_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datafilefinder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/datafilefinder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datafilefinder_8h__incl.svg -> ../html-full/datafilefinder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/position_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position_8h__incl.svg -> ../html-full/position_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ArrayRefWithPadding-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ArrayRefWithPadding-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ArrayRefWithPadding-members.xhtml -> ../html-full/classgmx_1_1ArrayRefWithPadding-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter.xhtml -> ../html-full/classgmx_1_1IFrameConverter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/updategroups_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/updategroups_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/updategroups_8h__incl.svg -> ../html-full/updategroups_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleManager-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/usergpuids_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/usergpuids_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/usergpuids_8h__incl.svg -> ../html-full/usergpuids_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisModule-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_analysisnbsearch.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_analysisnbsearch.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_analysisnbsearch.xhtml -> ../html-full/page_analysisnbsearch.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbc__aiuc__sycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pbc__aiuc__sycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbc__aiuc__sycl_8h__incl.svg -> ../html-full/pbc__aiuc__sycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabs.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tabs.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabs.css -> ../html-full/tabs.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/com_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/com_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/com_8h__incl.svg -> ../html-full/com_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLine-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLine-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLine-members.xhtml -> ../html-full/classgmx_1_1test_1_1CommandLine-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputStream.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream.xhtml -> ../html-full/classgmx_1_1TextInputStream.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000036_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000036_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000036_000002.xhtml -> ../html-full/dir_000036_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0aefc163fe06e931dd2f149958a61e72_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0aefc163fe06e931dd2f149958a61e72_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0aefc163fe06e931dd2f149958a61e72_dep.svg -> ../html-full/dir_0aefc163fe06e931dd2f149958a61e72_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/haloexchange_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/haloexchange_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/haloexchange_8h__incl.svg -> ../html-full/haloexchange_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverterenums_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/frameconverterenums_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverterenums_8h.xhtml -> ../html-full/frameconverterenums_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo-members.xhtml -> ../html-full/classgmx_1_1SelectionOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structDeviceInformation.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation.xhtml -> ../html-full/structDeviceInformation.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar__math_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/scalar__math_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar__math_8h__incl.svg -> ../html-full/scalar__math_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputStream.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream.xhtml -> ../html-full/classgmx_1_1TextOutputStream.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulatorBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorBuilder-members.xhtml -> ../html-full/classgmx_1_1SimulatorBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAnalysisData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisData-members.xhtml -> ../html-full/classgmx_1_1AbstractAnalysisData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right_1_1mapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1layout__right_1_1mapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right_1_1mapping-members.xhtml -> ../html-full/classgmx_1_1layout__right_1_1mapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyTerm-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyTerm-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyTerm-members.xhtml -> ../html-full/classgmx_1_1EnergyTerm-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData.xhtml -> ../html-full/classgmx_1_1PotentialPointData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggerBuilder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder.xhtml -> ../html-full/classgmx_1_1LoggerBuilder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/manager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/manager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/manager_8h__incl.svg -> ../html-full/manager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_cbb6801c5e414b597382fe4dc954b6d1_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_cbb6801c5e414b597382fe4dc954b6d1_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_cbb6801c5e414b597382fe4dc954b6d1_dep.svg -> ../html-full/dir_cbb6801c5e414b597382fe4dc954b6d1_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerImpl.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classGpuRegionTimerImpl.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerImpl.xhtml -> ../html-full/classGpuRegionTimerImpl.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2b7ade0811f8e64041419846b7254328_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_2b7ade0811f8e64041419846b7254328_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2b7ade0811f8e64041419846b7254328_dep.svg -> ../html-full/dir_2b7ade0811f8e64041419846b7254328_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionsOfType.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionsOfType.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionsOfType.xhtml -> ../html-full/structInteractionsOfType.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4b9e53d55f9e039e1cf3b481d5abf6a6_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4b9e53d55f9e039e1cf3b481d5abf6a6_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4b9e53d55f9e039e1cf3b481d5abf6a6_dep.svg -> ../html-full/dir_4b9e53d55f9e039e1cf3b481d5abf6a6_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c4da5f775985f85635625e7a0058704c_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c4da5f775985f85635625e7a0058704c_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c4da5f775985f85635625e7a0058704c_dep.svg -> ../html-full/dir_c4da5f775985f85635625e7a0058704c_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_843fb085a7ffaaff8607e2c539c5b0fe_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_843fb085a7ffaaff8607e2c539c5b0fe_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_843fb085a7ffaaff8607e2c539c5b0fe_dep.svg -> ../html-full/dir_843fb085a7ffaaff8607e2c539c5b0fe_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_5.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_5.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_5.svg -> ../html-full/msc_inline_mscgraph_5.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainLifetimeWorkload.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainLifetimeWorkload.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainLifetimeWorkload.xhtml -> ../html-full/classgmx_1_1DomainLifetimeWorkload.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_00ac45d032b1acf2e2418c9365820491_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_00ac45d032b1acf2e2418c9365820491_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_00ac45d032b1acf2e2418c9365820491_dep.svg -> ../html-full/dir_00ac45d032b1acf2e2418c9365820491_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/indexutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/indexutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/indexutil_8h__incl.svg -> ../html-full/indexutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6cc3f6633093836886a4ce2735dc640b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6cc3f6633093836886a4ce2735dc640b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6cc3f6633093836886a4ce2735dc640b_dep.svg -> ../html-full/dir_6cc3f6633093836886a4ce2735dc640b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainerwithsections_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioptionscontainerwithsections_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainerwithsections_8h__incl.svg -> ../html-full/ioptionscontainerwithsections_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_56293306df9b62cfc470e5d2417454ba_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_56293306df9b62cfc470e5d2417454ba_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_56293306df9b62cfc470e5d2417454ba_dep.svg -> ../html-full/dir_56293306df9b62cfc470e5d2417454ba_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_50c6cc2f8c6a84d23d5f2f05142ad0ee_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_50c6cc2f8c6a84d23d5f2f05142ad0ee_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_50c6cc2f8c6a84d23d5f2f05142ad0ee_dep.svg -> ../html-full/dir_50c6cc2f8c6a84d23d5f2f05142ad0ee_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MdrunnerBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MdrunnerBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MdrunnerBuilder-members.xhtml -> ../html-full/classgmx_1_1MdrunnerBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b252a48bab628016606f26349d339e0f_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b252a48bab628016606f26349d339e0f_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b252a48bab628016606f26349d339e0f_dep.svg -> ../html-full/dir_b252a48bab628016606f26349d339e0f_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pargs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pargs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pargs_8h__incl.svg -> ../html-full/pargs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1compat_1_1not__null-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1compat_1_1not__null-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1compat_1_1not__null-members.xhtml -> ../html-full/classgmx_1_1compat_1_1not__null-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionInfo__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1OptionInfo__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iframeconverter_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iframeconverter_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iframeconverter_8h.xhtml -> ../html-full/iframeconverter_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_3.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_3.svg -> ../html-full/msc_inline_mscgraph_3.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClHandle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ClHandle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClHandle.xhtml -> ../html-full/classgmx_1_1ClHandle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileOptions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DataFileOptions.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileOptions.xhtml -> ../html-full/classgmx_1_1DataFileOptions.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangePartitioning.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangePartitioning.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangePartitioning.xhtml -> ../html-full/classgmx_1_1RangePartitioning.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__memory_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simd__memory_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__memory_8h__incl.svg -> ../html-full/simd__memory_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000002.xhtml -> ../html-full/dir_000059_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Range.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Range.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Range.xhtml -> ../html-full/classgmx_1_1Range.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/logging_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/logging_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/logging_8h__incl.svg -> ../html-full/logging_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_85957c1083185c206e1047ce128800f7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_85957c1083185c206e1047ce128800f7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_85957c1083185c206e1047ce128800f7_dep.svg -> ../html-full/dir_85957c1083185c206e1047ce128800f7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PackedJClusterList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PackedJClusterList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PackedJClusterList.xhtml -> ../html-full/classgmx_1_1PackedJClusterList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeObjectBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeObjectBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_5.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_5.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_5.svg -> ../html-full/dot_inline_dotgraph_5.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000109_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000109_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000109_000002.xhtml -> ../html-full/dir_000109_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_onlinehelp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_onlinehelp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_onlinehelp.xhtml -> ../html-full/page_onlinehelp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IKeyValueTreeTransformRules.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IKeyValueTreeTransformRules.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IKeyValueTreeTransformRules.xhtml -> ../html-full/classgmx_1_1IKeyValueTreeTransformRules.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineModuleManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineModuleManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineModuleManager-members.xhtml -> ../html-full/classgmx_1_1CommandLineModuleManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_4.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_4.svg -> ../html-full/dot_inline_dotgraph_4.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1JClusterList.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1JClusterList.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1JClusterList.xhtml -> ../html-full/classgmx_1_1JClusterList.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/extensions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/extensions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/extensions_8h__incl.svg -> ../html-full/extensions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000047_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000047_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000047_000002.xhtml -> ../html-full/dir_000047_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000163_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000163_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000163_000002.xhtml -> ../html-full/dir_000163_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listed__forces__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/listed__forces__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/listed__forces__gpu_8h__incl.svg -> ../html-full/listed__forces__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommBackward-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainCommBackward-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommBackward-members.xhtml -> ../html-full/classgmx_1_1DomainCommBackward-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/symtab_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/symtab_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/symtab_8h__incl.svg -> ../html-full/symtab_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Device.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Device.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Device.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Device.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLineTestHelper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineTestHelper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1CommandLineTestHelper-members.xhtml -> ../html-full/classgmx_1_1test_1_1CommandLineTestHelper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64Fast-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme_8h__incl.svg -> ../html-full/pme_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo-members.xhtml -> ../html-full/classgmx_1_1StringOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__sparsematrix.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__sparsematrix.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__sparsematrix.xhtml -> ../html-full/structgmx__sparsematrix.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/valuestore_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/valuestore_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/valuestore_8h__incl.svg -> ../html-full/valuestore_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsvisitor_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionsvisitor_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsvisitor_8h__incl.svg -> ../html-full/optionsvisitor_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fc8f2d3524d8a074d3a03e1fb39d7972_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_fc8f2d3524d8a074d3a03e1fb39d7972_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fc8f2d3524d8a074d3a03e1fb39d7972_dep.svg -> ../html-full/dir_fc8f2d3524d8a074d3a03e1fb39d7972_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml -> ../html-full/dir_c967dac1b679d5762f622f5d0982f1b6.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_877c684fb5600b4b89c3294751bf03b1_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_877c684fb5600b4b89c3294751bf03b1_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_877c684fb5600b4b89c3294751bf03b1_dep.svg -> ../html-full/dir_877c684fb5600b4b89c3294751bf03b1_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_659a81188d057ddf97df9487bf5d3984_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_659a81188d057ddf97df9487bf5d3984_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_659a81188d057ddf97df9487bf5d3984_dep.svg -> ../html-full/dir_659a81188d057ddf97df9487bf5d3984_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tableinput_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tableinput_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tableinput_8h__incl.svg -> ../html-full/tableinput_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution-members.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a504950c834d58a27b0bd71a5abd3a11.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a504950c834d58a27b0bd71a5abd3a11.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a504950c834d58a27b0bd71a5abd3a11.xhtml -> ../html-full/dir_a504950c834d58a27b0bd71a5abd3a11.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPbcAiuc.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPbcAiuc.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPbcAiuc.xhtml -> ../html-full/structPbcAiuc.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t.xhtml -> ../html-full/structgmx__ffparams__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenameoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenameoption_8h__incl.svg -> ../html-full/filenameoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringContext.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MessageStringContext.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringContext.xhtml -> ../html-full/classgmx_1_1MessageStringContext.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo-members.xhtml -> ../html-full/classgmx_1_1SelectionFileOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPointSetRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataPointSetRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1extents-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1extents-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1extents-members.xhtml -> ../html-full/classgmx_1_1extents-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec__zones_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/domdec__zones_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec__zones_8h__incl.svg -> ../html-full/domdec__zones_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderOutput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput.xhtml -> ../html-full/classgmx_1_1ForceProviderOutput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioptionscontainer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioptionscontainer_8h__incl.svg -> ../html-full/ioptionscontainer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo-members.xhtml -> ../html-full/classgmx_1_1IntegerOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteraction.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structBondedInteraction.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteraction.xhtml -> ../html-full/structBondedInteraction.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleParallel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo-members.xhtml -> ../html-full/classgmx_1_1Int64OptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__settings_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__gpu__settings_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__settings_8h__incl.svg -> ../html-full/pme__gpu__settings_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo-members.xhtml -> ../html-full/classgmx_1_1BooleanOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_2.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_2.svg -> ../html-full/dot_inline_dotgraph_2.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo-members.xhtml -> ../html-full/classgmx_1_1EnumOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000004_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000004_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000004_000156.xhtml -> ../html-full/dir_000004_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nrjac_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h__incl.svg -> ../html-full/nrjac_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo-members.xhtml -> ../html-full/classgmx_1_1DoubleOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProxy.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomProxy.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProxy.xhtml -> ../html-full/classAtomProxy.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor.xhtml -> ../html-full/classgmx_1_1OptionsTypeVisitor.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo-members.xhtml -> ../html-full/classgmx_1_1FloatOptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StepWorkload-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StepWorkload-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StepWorkload-members.xhtml -> ../html-full/classgmx_1_1StepWorkload-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyterm_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/energyterm_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyterm_8h__incl.svg -> ../html-full/energyterm_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_70251a2c68847dfb31098c2d75e23710_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_70251a2c68847dfb31098c2d75e23710_dep.svg -> ../html-full/dir_70251a2c68847dfb31098c2d75e23710_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000033_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000033_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000033_000002.xhtml -> ../html-full/dir_000033_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationIterator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumerationIterator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationIterator.xhtml -> ../html-full/classgmx_1_1EnumerationIterator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/interactivetest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/interactivetest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/interactivetest_8h__incl.svg -> ../html-full/interactivetest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileManager-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestFileManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vsite_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/vsite_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vsite_8h__incl.svg -> ../html-full/vsite_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/disre_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/disre_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/disre_8h__incl.svg -> ../html-full/disre_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSimulationGroups.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups.xhtml -> ../html-full/structSimulationGroups.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nrjac_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8cpp.xhtml -> ../html-full/nrjac_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpWriterContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HelpWriterContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpWriterContext-members.xhtml -> ../html-full/classgmx_1_1HelpWriterContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IAnalysisDataModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IAnalysisDataModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IAnalysisDataModule-members.xhtml -> ../html-full/classgmx_1_1IAnalysisDataModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa3d41089d179a9faa2d238e52127bdd_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_fa3d41089d179a9faa2d238e52127bdd_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa3d41089d179a9faa2d238e52127bdd_dep.svg -> ../html-full/dir_fa3d41089d179a9faa2d238e52127bdd_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOption-members.xhtml -> ../html-full/classgmx_1_1AbstractOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeBuilder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeBuilder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeBuilder.xhtml -> ../html-full/classgmx_1_1KeyValueTreeBuilder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPreprocessingAtomTypes-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPreprocessingAtomTypes-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPreprocessingAtomTypes-members.xhtml -> ../html-full/classPreprocessingAtomTypes-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_dd2646bca52814177a26769babeebfd3_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_dd2646bca52814177a26769babeebfd3_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_dd2646bca52814177a26769babeebfd3_dep.svg -> ../html-full/dir_dd2646bca52814177a26769babeebfd3_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t.xhtml -> ../html-full/structgmx__moltype__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UnionFinder.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UnionFinder.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UnionFinder.xhtml -> ../html-full/classgmx_1_1UnionFinder.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyFunctionProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnergyFunctionProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyFunctionProperties-members.xhtml -> ../html-full/structgmx_1_1EnergyFunctionProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionInfo-members.xhtml -> ../html-full/classgmx_1_1OptionInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdmodulesnotifier_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> ../html-full/mdmodulesnotifier_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1QuadraticSplineTable-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QuadraticSplineTable-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1QuadraticSplineTable-members.xhtml -> ../html-full/classgmx_1_1QuadraticSplineTable-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ListOfLists-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ListOfLists-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ListOfLists-members.xhtml -> ../html-full/classgmx_1_1ListOfLists-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInputPointSet-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnalysisDataTestInputPointSet-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInputPointSet-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnalysisDataTestInputPointSet-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineHelpContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineHelpContext-members.xhtml -> ../html-full/classgmx_1_1CommandLineHelpContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__interaction__function.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__interaction__function.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__interaction__function.xhtml -> ../html-full/structt__interaction__function.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionManagerContainer.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionManagerContainer.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionManagerContainer.xhtml -> ../html-full/classgmx_1_1OptionManagerContainer.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForceHelperBuffers.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForceHelperBuffers.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForceHelperBuffers.xhtml -> ../html-full/classForceHelperBuffers.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/checkpointhandler_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/checkpointhandler_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/checkpointhandler_8h__incl.svg -> ../html-full/checkpointhandler_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestException-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError-members.xhtml -> ../html-full/classgmx_1_1MissingElementConnectionError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CubicSplineTable-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CubicSplineTable-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CubicSplineTable-members.xhtml -> ../html-full/classgmx_1_1CubicSplineTable-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError-members.xhtml -> ../html-full/classgmx_1_1InconsistentInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextWriter-members.xhtml -> ../html-full/classgmx_1_1TextWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1InstallationPrefixInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1InstallationPrefixInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1InstallationPrefixInfo.xhtml -> ../html-full/structgmx_1_1InstallationPrefixInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError-members.xhtml -> ../html-full/classgmx_1_1ElementNotFoundError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__sycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gputraits__sycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__sycl_8h__incl.svg -> ../html-full/gputraits__sycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError-members.xhtml -> ../html-full/classgmx_1_1ParallelConsistencyError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError-members.xhtml -> ../html-full/classgmx_1_1InvalidInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption-members.xhtml -> ../html-full/classgmx_1_1SelectionFileOption-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_11c14dcc939f3db0f53cf820932f0ca3_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_11c14dcc939f3db0f53cf820932f0ca3_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_11c14dcc939f3db0f53cf820932f0ca3_dep.svg -> ../html-full/dir_11c14dcc939f3db0f53cf820932f0ca3_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError-members.xhtml -> ../html-full/classgmx_1_1CheckpointError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnalysisDataTestFixture-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError-members.xhtml -> ../html-full/classgmx_1_1NotImplementedError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_11c14dcc939f3db0f53cf820932f0ca3.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_11c14dcc939f3db0f53cf820932f0ca3.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_11c14dcc939f3db0f53cf820932f0ca3.xhtml -> ../html-full/dir_11c14dcc939f3db0f53cf820932f0ca3.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1325f6f8c1f6104ccc769b084d339b79_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1325f6f8c1f6104ccc769b084d339b79_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1325f6f8c1f6104ccc769b084d339b79_dep.svg -> ../html-full/dir_1325f6f8c1f6104ccc769b084d339b79_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000101_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000002.xhtml -> ../html-full/dir_000101_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/awh_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh_8h__incl.svg -> ../html-full/awh_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/register_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/register_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/register_8h.xhtml -> ../html-full/register_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1LogicalProcessor.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1LogicalProcessor.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1LogicalProcessor.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1LogicalProcessor.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__utilitymodules.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__utilitymodules.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__utilitymodules.xhtml -> ../html-full/group__group__utilitymodules.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRulesScoped.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeTransformRulesScoped.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRulesScoped.xhtml -> ../html-full/classgmx_1_1KeyValueTreeTransformRulesScoped.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogEntryWriter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LogEntryWriter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogEntryWriter.xhtml -> ../html-full/classgmx_1_1LogEntryWriter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnalysisDataTestInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInput-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnalysisDataTestInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__coordinateio.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__coordinateio.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__coordinateio.svg -> ../html-full/group__module__coordinateio.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyInformation-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyInformation-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyInformation-members.xhtml -> ../html-full/classgmx_1_1TopologyInformation-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> ../html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution-members.xhtml -> ../html-full/classgmx_1_1NormalDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringCollector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MessageStringCollector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringCollector-members.xhtml -> ../html-full/classgmx_1_1MessageStringCollector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull__params_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pull__params_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull__params_8h__incl.svg -> ../html-full/pull__params_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution-members.xhtml -> ../html-full/classgmx_1_1GammaDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iserializer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iserializer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iserializer_8h__incl.svg -> ../html-full/iserializer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helptopic_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/helptopic_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helptopic_8h__incl.svg -> ../html-full/helptopic_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpu__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__utils_8h__incl.svg -> ../html-full/gpu__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__utilitymodules.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__utilitymodules.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__utilitymodules.svg -> ../html-full/group__group__utilitymodules.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError-members.xhtml -> ../html-full/classgmx_1_1SimulationInstabilityError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__output_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__output_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__output_8h__incl.svg -> ../html-full/pme__output_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NameOfTestFromTuple.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NameOfTestFromTuple.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NameOfTestFromTuple.xhtml -> ../html-full/classgmx_1_1test_1_1NameOfTestFromTuple.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fixedcapacityvector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fixedcapacityvector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fixedcapacityvector_8h__incl.svg -> ../html-full/fixedcapacityvector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumerationWrapper.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper.xhtml -> ../html-full/classgmx_1_1EnumerationWrapper.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput.xhtml -> ../html-full/classgmx_1_1LegacyInput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic-members.xhtml -> ../html-full/classgmx_1_1CompositeHelpTopic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Update-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Update-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Update-members.xhtml -> ../html-full/classgmx_1_1Update-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution-members.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculePatchDatabase.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase.xhtml -> ../html-full/structMoleculePatchDatabase.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError-members.xhtml -> ../html-full/classgmx_1_1ModularSimulatorError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ienergyanalysis_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ienergyanalysis_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ienergyanalysis_8h__incl.svg -> ../html-full/ienergyanalysis_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/loggerbuilder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/loggerbuilder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/loggerbuilder_8h__incl.svg -> ../html-full/loggerbuilder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle-members.xhtml -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h.xhtml -> ../html-full/gpuregiontimer_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000156.xhtml -> ../html-full/dir_000111_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sycl__kernel__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sycl__kernel__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sycl__kernel__utils_8h__incl.svg -> ../html-full/sycl__kernel__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FloatingPointTolerance-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FloatingPointTolerance-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FloatingPointTolerance-members.xhtml -> ../html-full/classgmx_1_1test_1_1FloatingPointTolerance-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter__inherit__graph.svg -> ../html-full/classgmx_1_1IOutputAdapter__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError-members.xhtml -> ../html-full/classgmx_1_1UserInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractCompositeHelpTopic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractCompositeHelpTopic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractCompositeHelpTopic-members.xhtml -> ../html-full/classgmx_1_1AbstractCompositeHelpTopic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c7469e0bc32a5001ddd4092216283533.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c7469e0bc32a5001ddd4092216283533.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c7469e0bc32a5001ddd4092216283533.xhtml -> ../html-full/dir_c7469e0bc32a5001ddd4092216283533.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionOfType-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionOfType-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionOfType-members.xhtml -> ../html-full/classInteractionOfType-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__ilist.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist.xhtml -> ../html-full/structt__ilist.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000002.xhtml -> ../html-full/dir_000017_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options-members.xhtml -> ../html-full/classgmx_1_1Options-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError-members.xhtml -> ../html-full/classgmx_1_1ToleranceError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError-members.xhtml -> ../html-full/classgmx_1_1InternalError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1Range_1_1iterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Range_1_1iterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1Range_1_1iterator-members.xhtml -> ../html-full/structgmx_1_1Range_1_1iterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError-members.xhtml -> ../html-full/classgmx_1_1FileIOError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__selection.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__selection.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__selection.svg -> ../html-full/group__module__selection.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError-members.xhtml -> ../html-full/classgmx_1_1RangeError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError-members.xhtml -> ../html-full/classgmx_1_1APIError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/devicebuffer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer_8h__incl.svg -> ../html-full/devicebuffer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_energyanalysisframework.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_energyanalysisframework.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_energyanalysisframework.xhtml -> ../html-full/page_energyanalysisframework.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f8cc18df0b24beefa155361cd440dcf3_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_f8cc18df0b24beefa155361cd440dcf3_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f8cc18df0b24beefa155361cd440dcf3_dep.svg -> ../html-full/dir_f8cc18df0b24beefa155361cd440dcf3_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__sci__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__sci__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__sci__t.xhtml -> ../html-full/structgmx_1_1nbnxn__sci__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInputFrame-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnalysisDataTestInputFrame-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnalysisDataTestInputFrame-members.xhtml -> ../html-full/classgmx_1_1test_1_1AnalysisDataTestInputFrame-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData.xhtml -> ../html-full/classgmx_1_1TopologyData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext-members.xhtml -> ../html-full/classgmx_1_1CommandLineProgramContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bonded_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bonded_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bonded_8h__incl.svg -> ../html-full/bonded_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Any-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Any-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Any-members.xhtml -> ../html-full/classgmx_1_1Any-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_9.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_9.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_9.svg -> ../html-full/msc_inline_mscgraph_9.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataValue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataValue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataValue-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataValue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nrjac_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h.xhtml -> ../html-full/nrjac_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__analysismodules.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__analysismodules.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__analysismodules.xhtml -> ../html-full/group__group__analysismodules.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dynsections.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dynsections.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dynsections.js -> ../html-full/dynsections.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel-members.xhtml -> ../html-full/classgmx_1_1TorchModel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CpuInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CpuInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CpuInfo-members.xhtml -> ../html-full/classgmx_1_1CpuInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_74ea7a20ddea31b7dbef0a77f192b496_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_74ea7a20ddea31b7dbef0a77f192b496_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_74ea7a20ddea31b7dbef0a77f192b496_dep.svg -> ../html-full/dir_74ea7a20ddea31b7dbef0a77f192b496_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionPosition-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionPosition-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionPosition-members.xhtml -> ../html-full/classgmx_1_1SelectionPosition-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager-members.xhtml -> ../html-full/classgmx_1_1SelectionOptionManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomentum.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomentum.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomentum.xhtml -> ../html-full/structSystemMomentum.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataStorage-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataStorage-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataStorage-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataStorage-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeBlockIndices.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeBlockIndices.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeBlockIndices.xhtml -> ../html-full/structMoleculeBlockIndices.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f8cc18df0b24beefa155361cd440dcf3.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_f8cc18df0b24beefa155361cd440dcf3.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f8cc18df0b24beefa155361cd440dcf3.xhtml -> ../html-full/dir_f8cc18df0b24beefa155361cd440dcf3.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerOwner.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggerOwner.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerOwner.xhtml -> ../html-full/classgmx_1_1LoggerOwner.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structdf__history__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structdf__history__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structdf__history__t-members.xhtml -> ../html-full/structdf__history__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFInt32.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32.xhtml -> ../html-full/classgmx_1_1SimdFInt32.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_6.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_6.svg -> ../html-full/dot_inline_dotgraph_6.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fileredirector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fileredirector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fileredirector_8h__incl.svg -> ../html-full/fileredirector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDensityMapHeader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader-members.xhtml -> ../html-full/structgmx_1_1MrcDensityMapHeader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2b08982de72be8ca36e1d07056b55a13_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_2b08982de72be8ca36e1d07056b55a13_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2b08982de72be8ca36e1d07056b55a13_dep.svg -> ../html-full/dir_2b08982de72be8ca36e1d07056b55a13_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09272e6ff19dc4e5390c3d279a55f783_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_09272e6ff19dc4e5390c3d279a55f783_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09272e6ff19dc4e5390c3d279a55f783_dep.svg -> ../html-full/dir_09272e6ff19dc4e5390c3d279a55f783_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GromacsException-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GromacsException-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GromacsException-members.xhtml -> ../html-full/classgmx_1_1GromacsException-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDInt32.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32.xhtml -> ../html-full/classgmx_1_1SimdDInt32.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ad1536f7cb730cdb3555fa848f54fbf7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ad1536f7cb730cdb3555fa848f54fbf7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ad1536f7cb730cdb3555fa848f54fbf7_dep.svg -> ../html-full/dir_ad1536f7cb730cdb3555fa848f54fbf7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ienergyanalysis_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ienergyanalysis_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ienergyanalysis_8h.xhtml -> ../html-full/ienergyanalysis_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__ocl_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__ocl_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__ocl_8h.xhtml -> ../html-full/gpuregiontimer__ocl_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignal.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignal.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignal.xhtml -> ../html-full/classgmx_1_1SimulationSignal.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle-members.xhtml -> ../html-full/classgmx_1_1OptionSectionHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd4__float_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__simd4__float_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd4__float_8h__incl.svg -> ../html-full/impl__reference__simd4__float_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd__float_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__simd__float_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd__float_8h__incl.svg -> ../html-full/impl__reference__simd__float_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesAtomsRedistributedSignal.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal.xhtml -> ../html-full/structgmx_1_1MDModulesAtomsRedistributedSignal.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1RefDataFilenameMaker.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1RefDataFilenameMaker.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1RefDataFilenameMaker.xhtml -> ../html-full/classgmx_1_1test_1_1RefDataFilenameMaker.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd4__double_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__simd4__double_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__simd4__double_8h__incl.svg -> ../html-full/impl__reference__simd4__double_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> ../html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_04cd3441b07d9cfaf10df2c92ee47400_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_04cd3441b07d9cfaf10df2c92ee47400_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_04cd3441b07d9cfaf10df2c92ee47400_dep.svg -> ../html-full/dir_04cd3441b07d9cfaf10df2c92ee47400_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/physicalnodecommunicator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/physicalnodecommunicator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/physicalnodecommunicator_8h__incl.svg -> ../html-full/physicalnodecommunicator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/alignedallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator_8h__incl.svg -> ../html-full/alignedallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/loggertest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/loggertest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/loggertest_8h__incl.svg -> ../html-full/loggertest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffersView-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceBuffersView-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffersView-members.xhtml -> ../html-full/classgmx_1_1ForceBuffersView-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForeignLambdaTerms-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForeignLambdaTerms-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForeignLambdaTerms-members.xhtml -> ../html-full/classForeignLambdaTerms-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/graph_legend.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/graph_legend.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/graph_legend.xhtml -> ../html-full/graph_legend.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HaloExchange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HaloExchange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HaloExchange-members.xhtml -> ../html-full/classgmx_1_1HaloExchange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineinit_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineinit_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineinit_8h__incl.svg -> ../html-full/cmdlineinit_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NumericalSplineTableInput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput.xhtml -> ../html-full/structgmx_1_1NumericalSplineTableInput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhood-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhood-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhood-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhood-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionfileoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionfileoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionfileoption_8h__incl.svg -> ../html-full/selectionfileoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculePatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatch-members.xhtml -> ../html-full/structMoleculePatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b3b10afaa073fb580ca3168487895926.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b3b10afaa073fb580ca3168487895926.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b3b10afaa073fb580ca3168487895926.xhtml -> ../html-full/dir_b3b10afaa073fb580ca3168487895926.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion-members.xhtml -> ../html-full/classgmx_1_1ProcessFrameConversion-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4DBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool.xhtml -> ../html-full/classgmx_1_1Simd4DBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4FBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool.xhtml -> ../html-full/classgmx_1_1Simd4FBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5a4b6336a2508428a9c6c3ca575d531.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a5a4b6336a2508428a9c6c3ca575d531.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5a4b6336a2508428a9c6c3ca575d531.xhtml -> ../html-full/dir_a5a4b6336a2508428a9c6c3ca575d531.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringCompare.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringCompare.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringCompare.xhtml -> ../html-full/classgmx_1_1StringCompare.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_awh.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_awh.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_awh.xhtml -> ../html-full/page_awh.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomIterator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomIterator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomIterator.xhtml -> ../html-full/classAtomIterator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataStorageFrame-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataStorageFrame-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataStorageFrame-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataStorageFrame-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Double.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double.xhtml -> ../html-full/classgmx_1_1Simd4Double.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FlagsTemplate-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FlagsTemplate-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FlagsTemplate-members.xhtml -> ../html-full/classgmx_1_1FlagsTemplate-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListIterator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListIterator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListIterator.xhtml -> ../html-full/classIListIterator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__packed__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayref_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arrayref_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/arrayref_8h__incl.svg -> ../html-full/arrayref_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Float.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float.xhtml -> ../html-full/classgmx_1_1Simd4Float.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverter_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/frameconverter_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/frameconverter_8h.xhtml -> ../html-full/frameconverter_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreePath-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreePath-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreePath-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreePath-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000100_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000100_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000100_000156.xhtml -> ../html-full/dir_000100_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDIBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool.xhtml -> ../html-full/classgmx_1_1SimdDIBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFIBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFIBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFIBool.xhtml -> ../html-full/classgmx_1_1SimdFIBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__filenm.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__filenm.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__filenm.xhtml -> ../html-full/structt__filenm.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDBool.xhtml -> ../html-full/classgmx_1_1SimdDBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDouble.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble.xhtml -> ../html-full/classgmx_1_1SimdDouble.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFBool.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFBool.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFBool.xhtml -> ../html-full/classgmx_1_1SimdFBool.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceOutputs.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceOutputs.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceOutputs.xhtml -> ../html-full/classgmx_1_1ForceOutputs.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSectionHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle-members.xhtml -> ../html-full/classgmx_1_1AbstractOptionSectionHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HostAllocationPolicy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HostAllocationPolicy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HostAllocationPolicy-members.xhtml -> ../html-full/classgmx_1_1HostAllocationPolicy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/range_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/range_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/range_8h__incl.svg -> ../html-full/range_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFloat.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat.xhtml -> ../html-full/classgmx_1_1SimdFloat.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structAtomsAdjacencyListElement.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structAtomsAdjacencyListElement.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structAtomsAdjacencyListElement.xhtml -> ../html-full/structAtomsAdjacencyListElement.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxsycl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmxsycl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxsycl_8h__incl.svg -> ../html-full/gmxsycl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdspan_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdspan_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdspan_8h__incl.svg -> ../html-full/mdspan_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classListedForces-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classListedForces-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classListedForces-members.xhtml -> ../html-full/classListedForces-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Cache.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Cache.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Cache.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Cache.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structFEPStateValue.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structFEPStateValue.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structFEPStateValue.xhtml -> ../html-full/structFEPStateValue.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Awh-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Awh-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Awh-members.xhtml -> ../html-full/classgmx_1_1Awh-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0b2931843d897cb82c2eadb28739c7d9.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0b2931843d897cb82c2eadb28739c7d9.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0b2931843d897cb82c2eadb28739c7d9.xhtml -> ../html-full/dir_0b2931843d897cb82c2eadb28739c7d9.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextReader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextReader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextReader-members.xhtml -> ../html-full/classgmx_1_1TextReader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setprecision_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setprecision_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setprecision_8h__incl.svg -> ../html-full/setprecision_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisHistogramSettingsInitializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisHistogramSettingsInitializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisHistogramSettingsInitializer-members.xhtml -> ../html-full/classgmx_1_1AnalysisHistogramSettingsInitializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule-members.xhtml -> ../html-full/classgmx_1_1RestraintMDModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/any_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/any_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/any_8h__incl.svg -> ../html-full/any_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroups.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UpdateGroups.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroups.xhtml -> ../html-full/classgmx_1_1UpdateGroups.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainerWithSections-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainerWithSections-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainerWithSections-members.xhtml -> ../html-full/classgmx_1_1IOptionsContainerWithSections-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classEwaldBoxZScaler.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler.xhtml -> ../html-full/classEwaldBoxZScaler.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsAssigner-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsAssigner-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsAssigner-members.xhtml -> ../html-full/classgmx_1_1OptionsAssigner-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000072_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000002.xhtml -> ../html-full/dir_000072_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringFormatter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringFormatter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringFormatter.xhtml -> ../html-full/classgmx_1_1StringFormatter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Numa.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Numa.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Numa.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Numa.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_40.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_49.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_40.png -> ../html-full/form_49.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1ProcessingUnit.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1ProcessingUnit.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1ProcessingUnit.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1ProcessingUnit.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__timing_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpu__timing_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpu__timing_8h__incl.svg -> ../html-full/gpu__timing_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1H5md-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1H5md-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1H5md-members.xhtml -> ../html-full/classgmx_1_1H5md-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapperSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextLineWrapperSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapperSettings-members.xhtml -> ../html-full/classgmx_1_1TextLineWrapperSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuHaloExchange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GpuHaloExchange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuHaloExchange-members.xhtml -> ../html-full/classgmx_1_1GpuHaloExchange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2.xhtml -> ../html-full/structgmx_1_1StaticLog2.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTableEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classStringTableEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTableEntry-members.xhtml -> ../html-full/classStringTableEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextTableFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextTableFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextTableFormatter-members.xhtml -> ../html-full/classgmx_1_1TextTableFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_40_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_49_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_40_dark.png -> ../html-full/form_49_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataHandle-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDModules-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDModules-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDModules-members.xhtml -> ../html-full/classgmx_1_1MDModules-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CpuInfo_1_1LogicalProcessor.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CpuInfo_1_1LogicalProcessor.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CpuInfo_1_1LogicalProcessor.xhtml -> ../html-full/structgmx_1_1CpuInfo_1_1LogicalProcessor.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ac0c8b41ed0200ca73ac5d4028c90ed3_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ac0c8b41ed0200ca73ac5d4028c90ed3_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ac0c8b41ed0200ca73ac5d4028c90ed3_dep.svg -> ../html-full/dir_ac0c8b41ed0200ca73ac5d4028c90ed3_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b6e3abb9460d35a8114626fa31e62381_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b6e3abb9460d35a8114626fa31e62381_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b6e3abb9460d35a8114626fa31e62381_dep.svg -> ../html-full/dir_b6e3abb9460d35a8114626fa31e62381_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HardwareTopology-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HardwareTopology-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HardwareTopology-members.xhtml -> ../html-full/classgmx_1_1HardwareTopology-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32474fd9548d0f2ad92adb149653ad10_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_32474fd9548d0f2ad92adb149653ad10_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32474fd9548d0f2ad92adb149653ad10_dep.svg -> ../html-full/dir_32474fd9548d0f2ad92adb149653ad10_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c3baf0acb816458bdf00c5bd3425f4d5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c3baf0acb816458bdf00c5bd3425f4d5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c3baf0acb816458bdf00c5bd3425f4d5.xhtml -> ../html-full/dir_c3baf0acb816458bdf00c5bd3425f4d5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BenchmarkSystem-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BenchmarkSystem-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BenchmarkSystem-members.xhtml -> ../html-full/structgmx_1_1BenchmarkSystem-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3706a2088846aeea3bf8dc88b1a89878_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3706a2088846aeea3bf8dc88b1a89878_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3706a2088846aeea3bf8dc88b1a89878_dep.svg -> ../html-full/dir_3706a2088846aeea3bf8dc88b1a89878_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t.xhtml -> ../html-full/structgmx__localtop__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxnPairlistCpu-members.xhtml -> ../html-full/structgmx_1_1NbnxnPairlistCpu-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FloatingPointDifference-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FloatingPointDifference-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FloatingPointDifference-members.xhtml -> ../html-full/classgmx_1_1test_1_1FloatingPointDifference-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Constraints-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Constraints-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Constraints-members.xhtml -> ../html-full/classgmx_1_1Constraints-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1TestSystem-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1TestSystem-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1TestSystem-members.xhtml -> ../html-full/structgmx_1_1test_1_1TestSystem-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringToEnumValueConverter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringToEnumValueConverter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringToEnumValueConverter.xhtml -> ../html-full/classgmx_1_1StringToEnumValueConverter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SelectionTopologyProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SelectionTopologyProperties-members.xhtml -> ../html-full/structgmx_1_1SelectionTopologyProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000161_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000161_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000161_000169.xhtml -> ../html-full/dir_000161_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomdecOptions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomdecOptions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomdecOptions-members.xhtml -> ../html-full/structgmx_1_1DomdecOptions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior-members.xhtml -> ../html-full/classgmx_1_1TimeUnitBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000010.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000010.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000010.xhtml -> ../html-full/dir_000023_000010.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPartialDeserializedTprFile.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile.xhtml -> ../html-full/structPartialDeserializedTprFile.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classekinstate__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classekinstate__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classekinstate__t-members.xhtml -> ../html-full/classekinstate__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestOptionsProvider.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestOptionsProvider.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestOptionsProvider.xhtml -> ../html-full/classgmx_1_1test_1_1TestOptionsProvider.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plot_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plot_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plot_8h__incl.svg -> ../html-full/plot_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structTpxFileHeader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structTpxFileHeader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structTpxFileHeader-members.xhtml -> ../html-full/structTpxFileHeader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogLevelHelper.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LogLevelHelper.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogLevelHelper.xhtml -> ../html-full/classgmx_1_1LogLevelHelper.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffers-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceBuffers-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceBuffers-members.xhtml -> ../html-full/classgmx_1_1ForceBuffers-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintManager-members.xhtml -> ../html-full/classgmx_1_1RestraintManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPositions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPositions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPositions-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPositions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GaussTransform3D-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GaussTransform3D-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GaussTransform3D-members.xhtml -> ../html-full/classgmx_1_1GaussTransform3D-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HashedMap-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HashedMap-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HashedMap-members.xhtml -> ../html-full/classgmx_1_1HashedMap-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DensitySimilarityMeasure-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensitySimilarityMeasure-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DensitySimilarityMeasure-members.xhtml -> ../html-full/classgmx_1_1DensitySimilarityMeasure-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gromacs_2mdrunutility_2freeenergy_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gromacs_2mdrunutility_2freeenergy_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gromacs_2mdrunutility_2freeenergy_8cpp.xhtml -> ../html-full/gromacs_2mdrunutility_2freeenergy_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_2.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_2.svg -> ../html-full/msc_inline_mscgraph_2.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PairlistSets-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PairlistSets-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PairlistSets-members.xhtml -> ../html-full/classgmx_1_1PairlistSets-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector-members.xhtml -> ../html-full/classgmx_1_1OutputSelector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ObservablesReducerBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ObservablesReducerBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ObservablesReducerBuilder-members.xhtml -> ../html-full/classgmx_1_1ObservablesReducerBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPdbAtomEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPdbAtomEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPdbAtomEntry-members.xhtml -> ../html-full/classPdbAtomEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000146_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000156.xhtml -> ../html-full/dir_000146_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_logging.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_logging.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_logging.xhtml -> ../html-full/page_logging.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01true_00_01true_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities-members.xhtml -> ../html-full/classgmx_1_1SetVelocities-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/graph_legend.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/graph_legend.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/graph_legend.svg -> ../html-full/graph_legend.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SettleData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SettleData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SettleData-members.xhtml -> ../html-full/classgmx_1_1SettleData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime-members.xhtml -> ../html-full/classgmx_1_1SetStartTime-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude.xhtml -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__analysismodules.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__group__analysismodules.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__group__analysismodules.svg -> ../html-full/group__group__analysismodules.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep-members.xhtml -> ../html-full/classgmx_1_1SetTimeStep-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000048_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000002.xhtml -> ../html-full/dir_000048_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroupsCog-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UpdateGroupsCog-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroupsCog-members.xhtml -> ../html-full/classgmx_1_1UpdateGroupsCog-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision-members.xhtml -> ../html-full/classgmx_1_1SetPrecision-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractoption_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractoption_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractoption_8h__incl.svg -> ../html-full/abstractoption_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringcompare_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringcompare_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringcompare_8h__incl.svg -> ../html-full/stringcompare_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PairSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PairSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PairSearch-members.xhtml -> ../html-full/classgmx_1_1PairSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fileptr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fileptr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fileptr_8h__incl.svg -> ../html-full/fileptr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1INNPotModel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1INNPotModel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1INNPotModel-members.xhtml -> ../html-full/classgmx_1_1INNPotModel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderOutput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput__coll__graph.svg -> ../html-full/classgmx_1_1ForceProviderOutput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000103_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000103_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000103_000002.xhtml -> ../html-full/dir_000103_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms-members.xhtml -> ../html-full/classgmx_1_1SetAtoms-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDataStatistics.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDataStatistics.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDataStatistics.xhtml -> ../html-full/structgmx_1_1MrcDataStatistics.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta.xhtml -> ../html-full/structSystemMomenta.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__excl__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__excl__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__excl__t.xhtml -> ../html-full/structgmx_1_1nbnxn__excl__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractoptionstorage_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractoptionstorage_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractoptionstorage_8h__incl.svg -> ../html-full/abstractoptionstorage_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox-members.xhtml -> ../html-full/classgmx_1_1SetBox-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces-members.xhtml -> ../html-full/classgmx_1_1SetForces-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/restraintmdmodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule_8h__incl.svg -> ../html-full/restraintmdmodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structObservablesHistory.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structObservablesHistory.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structObservablesHistory.xhtml -> ../html-full/structObservablesHistory.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__state__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__state__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__state__coll__graph.svg -> ../html-full/classt__state__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e04b7f51297172ca142021179e5c654_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1e04b7f51297172ca142021179e5c654_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e04b7f51297172ca142021179e5c654_dep.svg -> ../html-full/dir_1e04b7f51297172ca142021179e5c654_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000018_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000018_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000018_000100.xhtml -> ../html-full/dir_000018_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdSetZeroProxy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdSetZeroProxy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdSetZeroProxy-members.xhtml -> ../html-full/classgmx_1_1SimdSetZeroProxy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CrystallographicLabels.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CrystallographicLabels.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CrystallographicLabels.xhtml -> ../html-full/structgmx_1_1CrystallographicLabels.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CoordinatesAndBoxPreprocessed.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed.xhtml -> ../html-full/structgmx_1_1CoordinatesAndBoxPreprocessed.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_11_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_11_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_11_dark.png -> ../html-full/form_11_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d0b11f62be0359e75849112cad1766b1_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_d0b11f62be0359e75849112cad1766b1_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d0b11f62be0359e75849112cad1766b1_dep.svg -> ../html-full/dir_d0b11f62be0359e75849112cad1766b1_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textwriter_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h.xhtml -> ../html-full/textwriter_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ObservablesReducer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ObservablesReducer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ObservablesReducer-members.xhtml -> ../html-full/classgmx_1_1ObservablesReducer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextLineWrapper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper-members.xhtml -> ../html-full/classgmx_1_1TextLineWrapper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f3d3d9b005904145fe397b5d3a7ca8e3_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_f3d3d9b005904145fe397b5d3a7ca8e3_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_f3d3d9b005904145fe397b5d3a7ca8e3_dep.svg -> ../html-full/dir_f3d3d9b005904145fe397b5d3a7ca8e3_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_158ed0353e38094d0c19cad32861aa24_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_158ed0353e38094d0c19cad32861aa24_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_158ed0353e38094d0c19cad32861aa24_dep.svg -> ../html-full/dir_158ed0353e38094d0c19cad32861aa24_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1ForceSwitch_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__molblock__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__molblock__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__molblock__t.xhtml -> ../html-full/structgmx__molblock__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BinaryInformationSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BinaryInformationSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BinaryInformationSettings-members.xhtml -> ../html-full/classgmx_1_1BinaryInformationSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TranslateAndScale-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TranslateAndScale-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TranslateAndScale-members.xhtml -> ../html-full/classgmx_1_1TranslateAndScale-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01calculateEnergies_00_01InteractionModifiers_1_1PotSwitch_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerImpl-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classGpuRegionTimerImpl-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerImpl-members.xhtml -> ../html-full/classGpuRegionTimerImpl-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PmePpCommGpu-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PmePpCommGpu-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PmePpCommGpu-members.xhtml -> ../html-full/classgmx_1_1PmePpCommGpu-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConvertTprInfo.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConvertTprInfo.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConvertTprInfo.xhtml -> ../html-full/classgmx_1_1ConvertTprInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c3baf0acb816458bdf00c5bd3425f4d5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c3baf0acb816458bdf00c5bd3425f4d5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c3baf0acb816458bdf00c5bd3425f4d5_dep.svg -> ../html-full/dir_c3baf0acb816458bdf00c5bd3425f4d5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4b325a1c4aa1a0d0d08bd093b4d6ad41_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4b325a1c4aa1a0d0d08bd093b4d6ad41_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4b325a1c4aa1a0d0d08bd093b4d6ad41_dep.svg -> ../html-full/dir_4b325a1c4aa1a0d0d08bd093b4d6ad41_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_282c80b14554b834a9a7075b84e9e859_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_282c80b14554b834a9a7075b84e9e859_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_282c80b14554b834a9a7075b84e9e859_dep.svg -> ../html-full/dir_282c80b14554b834a9a7075b84e9e859_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OutputRequirements-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OutputRequirements-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OutputRequirements-members.xhtml -> ../html-full/structgmx_1_1OutputRequirements-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager-members.xhtml -> ../html-full/classgmx_1_1FileNameOptionManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSettleWaterTopology.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology.xhtml -> ../html-full/structSettleWaterTopology.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1RocfftPlan-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1RocfftPlan-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1RocfftPlan-members.xhtml -> ../html-full/structgmx_1_1RocfftPlan-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput-members.xhtml -> ../html-full/classgmx_1_1ForceProviderInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_62ff1a117c10471df83a8a405cf8e9d7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_62ff1a117c10471df83a8a405cf8e9d7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_62ff1a117c10471df83a8a405cf8e9d7_dep.svg -> ../html-full/dir_62ff1a117c10471df83a8a405cf8e9d7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threadaffinity_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/threadaffinity_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threadaffinity_8h__incl.svg -> ../html-full/threadaffinity_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6513af17b9abf563e9fdc3036ea9e5e8_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6513af17b9abf563e9fdc3036ea9e5e8_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6513af17b9abf563e9fdc3036ea9e5e8_dep.svg -> ../html-full/dir_6513af17b9abf563e9fdc3036ea9e5e8_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c312871c1abe68829c489bb9a03103ec_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c312871c1abe68829c489bb9a03103ec_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c312871c1abe68829c489bb9a03103ec_dep.svg -> ../html-full/dir_c312871c1abe68829c489bb9a03103ec_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTable-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classStringTable-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTable-members.xhtml -> ../html-full/classStringTable-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000034_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000002.xhtml -> ../html-full/dir_000034_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01false_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__symbuf.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf.xhtml -> ../html-full/structt__symbuf.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisModuleData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_27e3cf47a1c055c3b64f6b8548cd4795_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_27e3cf47a1c055c3b64f6b8548cd4795_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_27e3cf47a1c055c3b64f6b8548cd4795_dep.svg -> ../html-full/dir_27e3cf47a1c055c3b64f6b8548cd4795_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MembedHolder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MembedHolder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MembedHolder-members.xhtml -> ../html-full/classgmx_1_1MembedHolder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisHistogramSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisHistogramSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisHistogramSettings-members.xhtml -> ../html-full/classgmx_1_1AnalysisHistogramSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ff6231185987059d271135972f82570e_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ff6231185987059d271135972f82570e_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ff6231185987059d271135972f82570e_dep.svg -> ../html-full/dir_ff6231185987059d271135972f82570e_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator_3_01true_00_01InteractionModifiers_1_1PotShift_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classWarningHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classWarningHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classWarningHandler-members.xhtml -> ../html-full/classWarningHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_1.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_1.svg -> ../html-full/msc_inline_mscgraph_1.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/allocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/allocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/allocator_8h__incl.svg -> ../html-full/allocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PackedJClusterList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PackedJClusterList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PackedJClusterList-members.xhtml -> ../html-full/classgmx_1_1PackedJClusterList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinehelpcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpcontext_8h__incl.svg -> ../html-full/cmdlinehelpcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/register_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/register_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/register_8h__incl.svg -> ../html-full/register_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldTabulated_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_11.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_11.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_11.png -> ../html-full/form_11.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping.xhtml -> ../html-full/structt__mapping.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuTaskAssignments-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GpuTaskAssignments-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuTaskAssignments-members.xhtml -> ../html-full/classgmx_1_1GpuTaskAssignments-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AllocatorTest.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AllocatorTest.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AllocatorTest.xhtml -> ../html-full/classgmx_1_1test_1_1AllocatorTest.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__im__ei__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__im__ei__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__im__ei__t.xhtml -> ../html-full/structgmx_1_1nbnxn__im__ei__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPreprocessResidue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue-members.xhtml -> ../html-full/structPreprocessResidue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExponentialMovingAverageState.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1ExponentialMovingAverageState.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExponentialMovingAverageState.xhtml -> ../html-full/structgmx_1_1ExponentialMovingAverageState.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1VirtualSitesHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VirtualSitesHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1VirtualSitesHandler-members.xhtml -> ../html-full/classgmx_1_1VirtualSitesHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1NumaNode.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1NumaNode.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1NumaNode.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1NumaNode.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic-members.xhtml -> ../html-full/classgmx_1_1SimpleHelpTopic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__domdec.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__domdec.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__domdec.svg -> ../html-full/group__module__domdec.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1shakedata-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1shakedata-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1shakedata-members.xhtml -> ../html-full/structgmx_1_1shakedata-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile-members.xhtml -> ../html-full/classgmx_1_1TextOutputFile-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DevelopmentFeatureFlags.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DevelopmentFeatureFlags.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DevelopmentFeatureFlags.xhtml -> ../html-full/structgmx_1_1DevelopmentFeatureFlags.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommForward-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainCommForward-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainCommForward-members.xhtml -> ../html-full/classgmx_1_1DomainCommForward-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1NormalDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions-members.xhtml -> ../html-full/classInteractionDefinitions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile-members.xhtml -> ../html-full/classgmx_1_1TextInputFile-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1StringTestBase-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1StringTestBase-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1StringTestBase-members.xhtml -> ../html-full/classgmx_1_1test_1_1StringTestBase-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractSimpleHelpTopic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractSimpleHelpTopic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractSimpleHelpTopic-members.xhtml -> ../html-full/classgmx_1_1AbstractSimpleHelpTopic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hardwaretopology_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hardwaretopology_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hardwaretopology_8h__incl.svg -> ../html-full/hardwaretopology_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Core.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Core.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Core.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Core.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000108_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000002.xhtml -> ../html-full/dir_000108_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1GammaDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1InteractiveTestHelper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1InteractiveTestHelper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1InteractiveTestHelper-members.xhtml -> ../html-full/classgmx_1_1test_1_1InteractiveTestHelper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_68267d1309a1af8e8297ef4c3efbcdba.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_68267d1309a1af8e8297ef4c3efbcdba.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_68267d1309a1af8e8297ef4c3efbcdba.xhtml -> ../html-full/dir_68267d1309a1af8e8297ef4c3efbcdba.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Device-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Device-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Device-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Device-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensitySkewData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDensitySkewData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensitySkewData.xhtml -> ../html-full/structgmx_1_1MrcDensitySkewData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer__helpers_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpueventsynchronizer__helpers_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer__helpers_8cpp.xhtml -> ../html-full/gpueventsynchronizer__helpers_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior-members.xhtml -> ../html-full/classgmx_1_1SelectionOptionBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Mdrunner-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Mdrunner-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Mdrunner-members.xhtml -> ../html-full/classgmx_1_1Mdrunner-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GromppMtsOpts.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GromppMtsOpts.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GromppMtsOpts.xhtml -> ../html-full/structgmx_1_1GromppMtsOpts.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CompileTimeStringJoin.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CompileTimeStringJoin.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CompileTimeStringJoin.xhtml -> ../html-full/structgmx_1_1CompileTimeStringJoin.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__matrix-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__matrix-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__matrix-members.xhtml -> ../html-full/structt__matrix-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_26f117cf35af0cc558c2ac47db8ebfc7.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_26f117cf35af0cc558c2ac47db8ebfc7.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_26f117cf35af0cc558c2ac47db8ebfc7.xhtml -> ../html-full/dir_26f117cf35af0cc558c2ac47db8ebfc7.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__hip_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h__incl.svg -> ../html-full/gpuregiontimer__hip_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/logger_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/logger_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/logger_8h__incl.svg -> ../html-full/logger_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1RF_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_df09b5ba214e360ecb99468cfd14e9e7.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_df09b5ba214e360ecb99468cfd14e9e7.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_df09b5ba214e360ecb99468cfd14e9e7.xhtml -> ../html-full/dir_df09b5ba214e360ecb99468cfd14e9e7.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPair-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PairsearchWork-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PairsearchWork-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PairsearchWork-members.xhtml -> ../html-full/structgmx_1_1PairsearchWork-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRuleBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeTransformRuleBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRuleBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeTransformRuleBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/enumerationhelpers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/enumerationhelpers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/enumerationhelpers_8h__incl.svg -> ../html-full/enumerationhelpers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainLifetimeWorkload-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainLifetimeWorkload-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainLifetimeWorkload-members.xhtml -> ../html-full/classgmx_1_1DomainLifetimeWorkload-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DensityFittingForce-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingForce-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DensityFittingForce-members.xhtml -> ../html-full/classgmx_1_1DensityFittingForce-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithShiftForces-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceWithShiftForces-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithShiftForces-members.xhtml -> ../html-full/classgmx_1_1ForceWithShiftForces-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/replicaexchange_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/replicaexchange_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/replicaexchange_8h__incl.svg -> ../html-full/replicaexchange_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pargs-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__pargs-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pargs-members.xhtml -> ../html-full/structt__pargs-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__sycl_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__sycl_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__sycl_8h.xhtml -> ../html-full/device__event__sycl_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AnalyticalSplineTableInput.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AnalyticalSplineTableInput.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AnalyticalSplineTableInput.xhtml -> ../html-full/structgmx_1_1AnalyticalSplineTableInput.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ClHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClHandle-members.xhtml -> ../html-full/classgmx_1_1ClHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mtop__lookup_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mtop__lookup_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mtop__lookup_8h__incl.svg -> ../html-full/mtop__lookup_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAnalysisFrame-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAnalysisFrame-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAnalysisFrame-members.xhtml -> ../html-full/classgmx_1_1EnergyAnalysisFrame-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_12.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_12.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_12.svg -> ../html-full/msc_inline_mscgraph_12.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pbc-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__pbc-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__pbc-members.xhtml -> ../html-full/structt__pbc-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListProxy.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListProxy.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListProxy.xhtml -> ../html-full/classIListProxy.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeInformation-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation-members.xhtml -> ../html-full/structMoleculeInformation-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestFileOutputRedirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/menu.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/menu.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/menu.js -> ../html-full/menu.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1JClusterList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1JClusterList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1JClusterList-members.xhtml -> ../html-full/classgmx_1_1JClusterList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotSettings-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataPlotSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData__coll__graph.svg -> ../html-full/classgmx_1_1TopologyData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineHelpWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineHelpWriter-members.xhtml -> ../html-full/classgmx_1_1CommandLineHelpWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListRange.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListRange.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListRange.xhtml -> ../html-full/classIListRange.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationIterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumerationIterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationIterator-members.xhtml -> ../html-full/classgmx_1_1EnumerationIterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_acb6dee1ce56d1306a9910143bc22f09.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_acb6dee1ce56d1306a9910143bc22f09.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_acb6dee1ce56d1306a9910143bc22f09.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_acb6dee1ce56d1306a9910143bc22f09.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection-members.xhtml -> ../html-full/classgmx_1_1RepeatingOptionSection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/swapcoords_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/swapcoords_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/swapcoords_8h__incl.svg -> ../html-full/swapcoords_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDLogger-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger-members.xhtml -> ../html-full/classgmx_1_1MDLogger-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Machine-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Machine-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Machine-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Machine-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmx__lmcurve_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmx__lmcurve_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmx__lmcurve_8h__incl.svg -> ../html-full/gmx__lmcurve_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FlagTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1FlagTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structwallcc__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structwallcc__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structwallcc__t.xhtml -> ../html-full/structwallcc__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000093.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000093.xhtml -> ../html-full/dir_000025_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1accessor__basic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic-members.xhtml -> ../html-full/classgmx_1_1accessor__basic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000044_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000044_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000044_000069.xhtml -> ../html-full/dir_000044_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setstarttime_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setstarttime_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setstarttime_8h__incl.svg -> ../html-full/setstarttime_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/settimestep_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/settimestep_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/settimestep_8h__incl.svg -> ../html-full/settimestep_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/domdec_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/domdec_8h__incl.svg -> ../html-full/domdec_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution_1_1param__type-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerWrapper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classGpuRegionTimerWrapper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classGpuRegionTimerWrapper-members.xhtml -> ../html-full/classGpuRegionTimerWrapper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionsOfType-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionsOfType-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionsOfType-members.xhtml -> ../html-full/structInteractionsOfType-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1OutputSelectorDeathTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1OutputSelectorDeathTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorStateData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulatorStateData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorStateData-members.xhtml -> ../html-full/structgmx_1_1SimulatorStateData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1IEntry.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1IEntry.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1IEntry.xhtml -> ../html-full/structt__nblist_1_1IEntry.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nonbonded__bench_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nonbonded__bench_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nonbonded__bench_8h__incl.svg -> ../html-full/nonbonded__bench_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000170.xhtml -> ../html-full/dir_000135_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyGroupsPerCluster-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyGroupsPerCluster-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyGroupsPerCluster-members.xhtml -> ../html-full/classgmx_1_1EnergyGroupsPerCluster-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DeviceStreamManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DeviceStreamManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DeviceStreamManager-members.xhtml -> ../html-full/classgmx_1_1DeviceStreamManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumClassSuitsEnumerationArray.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumClassSuitsEnumerationArray.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumClassSuitsEnumerationArray.xhtml -> ../html-full/classgmx_1_1EnumClassSuitsEnumerationArray.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml -> ../html-full/dir_55e6b9bceb5e3e08725efcf4929777ec.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/txtdump_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/txtdump_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/txtdump_8h__incl.svg -> ../html-full/txtdump_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomRange.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomRange.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomRange.xhtml -> ../html-full/classAtomRange.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/compare_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/compare_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/compare_8h__incl.svg -> ../html-full/compare_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/functions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_8h__incl.svg -> ../html-full/functions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceWithVirial-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial-members.xhtml -> ../html-full/classgmx_1_1ForceWithVirial-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IEnergyAnalysis-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IEnergyAnalysis-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IEnergyAnalysis-members.xhtml -> ../html-full/classgmx_1_1IEnergyAnalysis-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDDBalanceRegionHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classDDBalanceRegionHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDDBalanceRegionHandler-members.xhtml -> ../html-full/classDDBalanceRegionHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1LogicalProcessor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1LogicalProcessor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1LogicalProcessor-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1LogicalProcessor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structReplicaExchangeParameters.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structReplicaExchangeParameters.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structReplicaExchangeParameters.xhtml -> ../html-full/structReplicaExchangeParameters.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000046_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000046_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000046_000002.xhtml -> ../html-full/dir_000046_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/idef_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/idef_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/idef_8h__incl.svg -> ../html-full/idef_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml -> ../html-full/classgmx_1_1TrajectoryAnalysisCommandLineRunner-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Package.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Package.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Package.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Package.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GridDimensions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GridDimensions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GridDimensions-members.xhtml -> ../html-full/structgmx_1_1GridDimensions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream-members.xhtml -> ../html-full/classgmx_1_1StringInputStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e6ddf929e6679f18ebcc713bf7c5cec_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1e6ddf929e6679f18ebcc713bf7c5cec_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e6ddf929e6679f18ebcc713bf7c5cec_dep.svg -> ../html-full/dir_1e6ddf929e6679f18ebcc713bf7c5cec_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestReferenceData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestReferenceData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestReferenceData-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestReferenceData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesWriteCheckpointData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData.xhtml -> ../html-full/structgmx_1_1MDModulesWriteCheckpointData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000043_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000043_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000043_000002.xhtml -> ../html-full/dir_000043_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000162.xhtml -> ../html-full/dir_000025_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000045_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000002.xhtml -> ../html-full/dir_000045_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typetraits_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/typetraits_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typetraits_8h.xhtml -> ../html-full/typetraits_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8cpp.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nvshmem__utils_8cpp.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nvshmem__utils_8cpp.xhtml -> ../html-full/nvshmem__utils_8cpp.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError__inherit__graph.svg -> ../html-full/classgmx_1_1ModularSimulatorError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineModule-members.xhtml -> ../html-full/classgmx_1_1ICommandLineModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExceptionInitializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInitializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExceptionInitializer-members.xhtml -> ../html-full/classgmx_1_1ExceptionInitializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeUniformArrayBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeUniformArrayBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeUniformArrayBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeUniformArrayBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3d71ad7d27d849c1edfa7e85354eafed_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3d71ad7d27d849c1edfa7e85354eafed_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3d71ad7d27d849c1edfa7e85354eafed_dep.svg -> ../html-full/dir_3d71ad7d27d849c1edfa7e85354eafed_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcherSettings__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ITextBlockMatcherSettings__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcherSettings__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1ITextBlockMatcherSettings__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PmeForceSenderGpu-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PmeForceSenderGpu-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PmeForceSenderGpu-members.xhtml -> ../html-full/classgmx_1_1PmeForceSenderGpu-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestFileInputRedirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitManager-members.xhtml -> ../html-full/classgmx_1_1TimeUnitManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysissettings_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysissettings_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysissettings_8h__incl.svg -> ../html-full/analysissettings_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOutputAdapter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOutputAdapter-members.xhtml -> ../html-full/classgmx_1_1IOutputAdapter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_16.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_16.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_16.png -> ../html-full/form_16.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorEnv-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulatorEnv-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorEnv-members.xhtml -> ../html-full/classgmx_1_1SimulatorEnv-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01useEnergyGroups_00_01false_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000158_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000158_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000158_000170.xhtml -> ../html-full/dir_000158_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000032_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000032_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000032_000002.xhtml -> ../html-full/dir_000032_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx__ga2la__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx__ga2la__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx__ga2la__t-members.xhtml -> ../html-full/classgmx__ga2la__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000044_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000044_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000044_000170.xhtml -> ../html-full/dir_000044_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1PrefixFormatter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter.xhtml -> ../html-full/structgmx_1_1test_1_1PrefixFormatter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1no__delete.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1no__delete.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1no__delete.xhtml -> ../html-full/structgmx_1_1no__delete.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__nodecomm__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t.xhtml -> ../html-full/structgmx__nodecomm__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__index__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__index__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__index__t.xhtml -> ../html-full/structgmx__ana__index__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IProgramContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IProgramContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IProgramContext-members.xhtml -> ../html-full/classgmx_1_1IProgramContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setvelocities_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setvelocities_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setvelocities_8h__incl.svg -> ../html-full/setvelocities_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectArrayBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeObjectArrayBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeObjectArrayBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeObjectArrayBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000024_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000100.xhtml -> ../html-full/dir_000024_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatFromFileReader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MrcDensityMapOfFloatFromFileReader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatFromFileReader-members.xhtml -> ../html-full/classgmx_1_1MrcDensityMapOfFloatFromFileReader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5de40b585e9aa7d4c00bdcb37e5b399d.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_5de40b585e9aa7d4c00bdcb37e5b399d.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5de40b585e9aa7d4c00bdcb37e5b399d.xhtml -> ../html-full/dir_5de40b585e9aa7d4c00bdcb37e5b399d.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameHeader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameHeader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameHeader-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameHeader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setforces_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setforces_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setforces_8h__incl.svg -> ../html-full/setforces_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__nblist-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classt__nblist-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classt__nblist-members.xhtml -> ../html-full/classt__nblist-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000063.xhtml -> ../html-full/dir_000023_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Range-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Range-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Range-members.xhtml -> ../html-full/classgmx_1_1Range-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000029_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000029_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000029_000002.xhtml -> ../html-full/dir_000029_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomsetmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/localatomsetmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomsetmanager_8h__incl.svg -> ../html-full/localatomsetmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000031_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000002.xhtml -> ../html-full/dir_000031_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteraction-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structBondedInteraction-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteraction-members.xhtml -> ../html-full/structBondedInteraction-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRulesScoped-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeTransformRulesScoped-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeTransformRulesScoped-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeTransformRulesScoped-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/groupcoord_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/groupcoord_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/groupcoord_8h__incl.svg -> ../html-full/groupcoord_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialMovingAverage-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialMovingAverage-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialMovingAverage-members.xhtml -> ../html-full/classgmx_1_1ExponentialMovingAverage-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExclusionBlock.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1ExclusionBlock.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExclusionBlock.xhtml -> ../html-full/structgmx_1_1ExclusionBlock.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__ocl_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__ocl_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__ocl_8h.xhtml -> ../html-full/device__event__ocl_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPreprocessingBondAtomType-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPreprocessingBondAtomType-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPreprocessingBondAtomType-members.xhtml -> ../html-full/classPreprocessingBondAtomType-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000071.xhtml -> ../html-full/dir_000021_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structWaterMolecule.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structWaterMolecule.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structWaterMolecule.xhtml -> ../html-full/structWaterMolecule.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMDModule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IMDModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMDModule-members.xhtml -> ../html-full/classgmx_1_1IMDModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Allocator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Allocator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Allocator-members.xhtml -> ../html-full/classgmx_1_1Allocator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer__helpers_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpueventsynchronizer__helpers_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpueventsynchronizer__helpers_8cpp__incl.svg -> ../html-full/gpueventsynchronizer__helpers_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignaller-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignaller-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignaller-members.xhtml -> ../html-full/classgmx_1_1SimulationSignaller-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__t.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingBroadcast.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesCheckpointReadingBroadcast.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingBroadcast.xhtml -> ../html-full/structgmx_1_1MDModulesCheckpointReadingBroadcast.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MtsLevel.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MtsLevel.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MtsLevel.xhtml -> ../html-full/structgmx_1_1MtsLevel.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionList-members.xhtml -> ../html-full/structInteractionList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GpuTaskMapping.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GpuTaskMapping.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GpuTaskMapping.xhtml -> ../html-full/structgmx_1_1GpuTaskMapping.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IHelpTopic-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IHelpTopic-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IHelpTopic-members.xhtml -> ../html-full/classgmx_1_1IHelpTopic-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_16_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_16_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_16_dark.png -> ../html-full/form_16_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000091_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000091_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000091_000002.xhtml -> ../html-full/dir_000091_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000030_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000030_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000030_000170.xhtml -> ../html-full/dir_000030_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000097_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000169.xhtml -> ../html-full/dir_000097_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangePartitioning-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangePartitioning-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangePartitioning-members.xhtml -> ../html-full/classgmx_1_1RangePartitioning-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalTopologyChecker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LocalTopologyChecker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalTopologyChecker-members.xhtml -> ../html-full/classgmx_1_1LocalTopologyChecker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000030_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000030_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000030_000069.xhtml -> ../html-full/dir_000030_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters.xhtml -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textwriter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h__incl.svg -> ../html-full/textwriter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorEnv__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulatorEnv__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulatorEnv__coll__graph.svg -> ../html-full/classgmx_1_1SimulatorEnv__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t-members.xhtml -> ../html-full/structgmx__moltype__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PhysicalNodeCommunicator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PhysicalNodeCommunicator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PhysicalNodeCommunicator-members.xhtml -> ../html-full/classgmx_1_1PhysicalNodeCommunicator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000093.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000093.xhtml -> ../html-full/dir_000065_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000060_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000060_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000060_000002.xhtml -> ../html-full/dir_000060_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/utility_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/utility_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/utility_8h.xhtml -> ../html-full/utility_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1QMInputFileName.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1QMInputFileName.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1QMInputFileName.xhtml -> ../html-full/structgmx_1_1QMInputFileName.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000002.xhtml -> ../html-full/dir_000087_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IRestraintPotential-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IRestraintPotential-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IRestraintPotential-members.xhtml -> ../html-full/classgmx_1_1IRestraintPotential-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineprogramcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineprogramcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineprogramcontext_8h__incl.svg -> ../html-full/cmdlineprogramcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml -> ../html-full/classgmx_1_1ICommandLineOptionsModuleSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HaloMpiRequests.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HaloMpiRequests.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HaloMpiRequests.xhtml -> ../html-full/structgmx_1_1HaloMpiRequests.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainer-members.xhtml -> ../html-full/classgmx_1_1IOptionsContainer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__pos__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__pos__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__pos__t-members.xhtml -> ../html-full/structgmx__ana__pos__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputAdapterContainer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputAdapterContainer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputAdapterContainer-members.xhtml -> ../html-full/classgmx_1_1OutputAdapterContainer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef-members.xhtml -> ../html-full/structt__idef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000082_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000082_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000082_000169.xhtml -> ../html-full/dir_000082_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileFinder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DataFileFinder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileFinder-members.xhtml -> ../html-full/classgmx_1_1DataFileFinder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000000_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000000_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000000_000169.xhtml -> ../html-full/dir_000000_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1FilteringExactTextMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000079_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000079_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000079_000100.xhtml -> ../html-full/dir_000079_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPbcAiuc-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPbcAiuc-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPbcAiuc-members.xhtml -> ../html-full/structPbcAiuc-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionListHandle.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionListHandle.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionListHandle.xhtml -> ../html-full/structInteractionListHandle.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1LoggerTestHelper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1LoggerTestHelper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1LoggerTestHelper-members.xhtml -> ../html-full/classgmx_1_1test_1_1LoggerTestHelper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyNameUnit.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnergyNameUnit.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyNameUnit.xhtml -> ../html-full/structgmx_1_1EnergyNameUnit.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_modulegraph.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_modulegraph.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_modulegraph.xhtml -> ../html-full/page_modulegraph.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000064_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000064_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000064_000170.xhtml -> ../html-full/dir_000064_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeValueBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeValueBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeValueBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeValueBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProxy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomProxy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProxy-members.xhtml -> ../html-full/classAtomProxy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor-members.xhtml -> ../html-full/classgmx_1_1OptionsModifyingTypeVisitor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsBehaviorCollection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsBehaviorCollection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsBehaviorCollection-members.xhtml -> ../html-full/classgmx_1_1OptionsBehaviorCollection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter-members.xhtml -> ../html-full/classgmx_1_1IFrameConverter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_18.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_18.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_18.png -> ../html-full/form_18.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ga2la__t_1_1Entry.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry.xhtml -> ../html-full/structgmx__ga2la__t_1_1Entry.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__sci__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__sci__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__sci__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__sci__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainDecompositionBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainDecompositionBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainDecompositionBuilder-members.xhtml -> ../html-full/classgmx_1_1DomainDecompositionBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_010_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_010_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_010_01_4.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_010_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__sycl_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__sycl_8h.xhtml -> ../html-full/gpuregiontimer__sycl_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000170.xhtml -> ../html-full/dir_000017_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSet-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LocalAtomSet-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSet-members.xhtml -> ../html-full/classgmx_1_1LocalAtomSet-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IdentityFormatter.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IdentityFormatter.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IdentityFormatter.xhtml -> ../html-full/classgmx_1_1IdentityFormatter.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e8cb953fa5002f117153ad2af439d992_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_e8cb953fa5002f117153ad2af439d992_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e8cb953fa5002f117153ad2af439d992_dep.svg -> ../html-full/dir_e8cb953fa5002f117153ad2af439d992_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/seed_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/seed_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/seed_8h__incl.svg -> ../html-full/seed_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1JEntry.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1JEntry.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1JEntry.xhtml -> ../html-full/structt__nblist_1_1JEntry.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml -> ../html-full/classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1KeyValueTreeBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1KeyValueTreeBuilder-members.xhtml -> ../html-full/classgmx_1_1KeyValueTreeBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__coordinate__receiver__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__coordinate__receiver__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__coordinate__receiver__gpu_8h__incl.svg -> ../html-full/pme__coordinate__receiver__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ReadCheckpointDataHolder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ReadCheckpointDataHolder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ReadCheckpointDataHolder-members.xhtml -> ../html-full/classgmx_1_1ReadCheckpointDataHolder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSection-members.xhtml -> ../html-full/classgmx_1_1AbstractOptionSection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__force__sender__gpu_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__force__sender__gpu_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__force__sender__gpu_8h__incl.svg -> ../html-full/pme__force__sender__gpu_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainPairComm-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomainPairComm-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DomainPairComm-members.xhtml -> ../html-full/classgmx_1_1DomainPairComm-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000002.xhtml -> ../html-full/dir_000135_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c7469e0bc32a5001ddd4092216283533_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c7469e0bc32a5001ddd4092216283533_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c7469e0bc32a5001ddd4092216283533_dep.svg -> ../html-full/dir_c7469e0bc32a5001ddd4092216283533_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviders-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviders-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviders-members.xhtml -> ../html-full/classgmx_1_1ForceProviders-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Cache-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Cache-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Cache-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Cache-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__indexmap__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__indexmap__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__indexmap__t-members.xhtml -> ../html-full/structgmx__ana__indexmap__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogEntryWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LogEntryWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogEntryWriter-members.xhtml -> ../html-full/classgmx_1_1LogEntryWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroups-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UpdateGroups-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UpdateGroups-members.xhtml -> ../html-full/classgmx_1_1UpdateGroups-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_18_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_18_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_18_dark.png -> ../html-full/form_18_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork_1_1IClusterData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AtomPair.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AtomPair.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AtomPair.xhtml -> ../html-full/structgmx_1_1AtomPair.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDAtoms-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDAtoms-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDAtoms-members.xhtml -> ../html-full/classgmx_1_1MDAtoms-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4de8cf73220cc1861f39a5eeca0e23d2_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4de8cf73220cc1861f39a5eeca0e23d2_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4de8cf73220cc1861f39a5eeca0e23d2_dep.svg -> ../html-full/dir_4de8cf73220cc1861f39a5eeca0e23d2_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__onlinehelp.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__onlinehelp.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__onlinehelp.svg -> ../html-full/group__module__onlinehelp.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1fe0162ed265ecffa5da2d1611f0653a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1fe0162ed265ecffa5da2d1611f0653a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1fe0162ed265ecffa5da2d1611f0653a_dep.svg -> ../html-full/dir_1fe0162ed265ecffa5da2d1611f0653a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor-members.xhtml -> ../html-full/classgmx_1_1OptionsTypeVisitor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationContext-members.xhtml -> ../html-full/classgmx_1_1SimulationContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t-members.xhtml -> ../html-full/structgmx__ffparams__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0b2931843d897cb82c2eadb28739c7d9_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0b2931843d897cb82c2eadb28739c7d9_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0b2931843d897cb82c2eadb28739c7d9_dep.svg -> ../html-full/dir_0b2931843d897cb82c2eadb28739c7d9_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5c77c9cbe1c15cead2d534c2f9c41bfa_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_5c77c9cbe1c15cead2d534c2f9c41bfa_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5c77c9cbe1c15cead2d534c2f9c41bfa_dep.svg -> ../html-full/dir_5c77c9cbe1c15cead2d534c2f9c41bfa_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineParser-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineParser-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineParser-members.xhtml -> ../html-full/classgmx_1_1CommandLineParser-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__hip_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h.xhtml -> ../html-full/gpuregiontimer__hip_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ModuleSelection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection-members.xhtml -> ../html-full/classgmx_1_1test_1_1ModuleSelection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1ConfMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_bd52bb3a95340951d64175ed5b645be7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_bd52bb3a95340951d64175ed5b645be7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_bd52bb3a95340951d64175ed5b645be7_dep.svg -> ../html-full/dir_bd52bb3a95340951d64175ed5b645be7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_54b0c1074c8acf20942826c8ccd0dfe5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_54b0c1074c8acf20942826c8ccd0dfe5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_54b0c1074c8acf20942826c8ccd0dfe5_dep.svg -> ../html-full/dir_54b0c1074c8acf20942826c8ccd0dfe5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPpRanks.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPpRanks.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPpRanks.xhtml -> ../html-full/structPpRanks.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMdpOptionProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IMdpOptionProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMdpOptionProvider-members.xhtml -> ../html-full/classgmx_1_1IMdpOptionProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_011_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_011_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_011_01_4.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_011_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_96ab0e0c3487cfe17417b7953707b649_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_96ab0e0c3487cfe17417b7953707b649_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_96ab0e0c3487cfe17417b7953707b649_dep.svg -> ../html-full/dir_96ab0e0c3487cfe17417b7953707b649_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointHandler-members.xhtml -> ../html-full/classgmx_1_1CheckpointHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000170.xhtml -> ../html-full/dir_000111_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingDataOnMain.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesCheckpointReadingDataOnMain.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingDataOnMain.xhtml -> ../html-full/structgmx_1_1MDModulesCheckpointReadingDataOnMain.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionmanagercontainer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionmanagercontainer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionmanagercontainer_8h__incl.svg -> ../html-full/optionmanagercontainer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmap__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmap__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmap__t.xhtml -> ../html-full/structgmx__cmap__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1XvgMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyCalculationFrequencyErrors-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyCalculationFrequencyErrors-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyCalculationFrequencyErrors-members.xhtml -> ../html-full/classgmx_1_1EnergyCalculationFrequencyErrors-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__trajectoryanalysis.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__trajectoryanalysis.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__trajectoryanalysis.svg -> ../html-full/group__module__trajectoryanalysis.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__xpmelmt.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__xpmelmt.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__xpmelmt.xhtml -> ../html-full/structt__xpmelmt.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml -> ../html-full/classgmx_1_1AnalysisNeighborhoodPairSearch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WholeMoleculeTransform-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1WholeMoleculeTransform-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WholeMoleculeTransform-members.xhtml -> ../html-full/classgmx_1_1WholeMoleculeTransform-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeSolve-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPmeSolve-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeSolve-members.xhtml -> ../html-full/classPmeSolve-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000064_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000064_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000064_000069.xhtml -> ../html-full/dir_000064_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000071.xhtml -> ../html-full/dir_000111_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection-members.xhtml -> ../html-full/classgmx_1_1OptionSection-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structIndexGroup.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structIndexGroup.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structIndexGroup.xhtml -> ../html-full/structIndexGroup.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerOwner-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggerOwner-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerOwner-members.xhtml -> ../html-full/classgmx_1_1LoggerOwner-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structNumPmeDomains.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structNumPmeDomains.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structNumPmeDomains.xhtml -> ../html-full/structNumPmeDomains.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingIterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingIterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingIterator-members.xhtml -> ../html-full/classgmx_1_1OptionsModifyingIterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggerBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LoggerBuilder-members.xhtml -> ../html-full/classgmx_1_1LoggerBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumerationWrapper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper-members.xhtml -> ../html-full/classgmx_1_1EnumerationWrapper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__interaction__function-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__interaction__function-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__interaction__function-members.xhtml -> ../html-full/structt__interaction__function-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Site-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Site-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Site-members.xhtml -> ../html-full/classgmx_1_1Site-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tprfilegenerator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tprfilegenerator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tprfilegenerator_8h__incl.svg -> ../html-full/tprfilegenerator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_6.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_6.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_6.png -> ../html-full/form_6.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_1.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_1.svg -> ../html-full/dot_inline_dotgraph_1.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__hip_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__hip_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__hip_8h.xhtml -> ../html-full/device__event__hip_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/strdb_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/strdb_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/strdb_8h__incl.svg -> ../html-full/strdb_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HelpManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpManager-members.xhtml -> ../html-full/classgmx_1_1HelpManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DirectoryEnumerator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DirectoryEnumerator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DirectoryEnumerator-members.xhtml -> ../html-full/classgmx_1_1DirectoryEnumerator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setbox_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setbox_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setbox_8h__incl.svg -> ../html-full/setbox_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeBlockIndices-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeBlockIndices-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeBlockIndices-members.xhtml -> ../html-full/structMoleculeBlockIndices-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cstringutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cstringutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cstringutil_8h__incl.svg -> ../html-full/cstringutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProperties-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomProperties-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomProperties-members.xhtml -> ../html-full/classAtomProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__enerdata__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t-members.xhtml -> ../html-full/structgmx__enerdata__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_85957c1083185c206e1047ce128800f7.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_85957c1083185c206e1047ce128800f7.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_85957c1083185c206e1047ce128800f7.xhtml -> ../html-full/dir_85957c1083185c206e1047ce128800f7.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_6_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_6_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_6_dark.png -> ../html-full/form_6_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structObservablesHistory-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structObservablesHistory-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structObservablesHistory-members.xhtml -> ../html-full/structObservablesHistory-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000095_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000095_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000095_000071.xhtml -> ../html-full/dir_000095_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PageAlignedAllocationPolicy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PageAlignedAllocationPolicy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PageAlignedAllocationPolicy-members.xhtml -> ../html-full/classgmx_1_1PageAlignedAllocationPolicy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml -> ../html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000054_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000170.xhtml -> ../html-full/dir_000054_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream-members.xhtml -> ../html-full/classgmx_1_1StandardInputStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000020_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000020_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000020_000169.xhtml -> ../html-full/dir_000020_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatReader-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MrcDensityMapOfFloatReader-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatReader-members.xhtml -> ../html-full/classgmx_1_1MrcDensityMapOfFloatReader-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__multisim__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__multisim__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__multisim__t-members.xhtml -> ../html-full/structgmx__multisim__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/unique__cptr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/unique__cptr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/unique__cptr_8h__incl.svg -> ../html-full/unique__cptr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionManagerContainer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionManagerContainer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionManagerContainer-members.xhtml -> ../html-full/classgmx_1_1OptionManagerContainer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NameOfTestFromTuple-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NameOfTestFromTuple-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NameOfTestFromTuple-members.xhtml -> ../html-full/classgmx_1_1test_1_1NameOfTestFromTuple-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput-members.xhtml -> ../html-full/classgmx_1_1LegacyInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structLocalSettleData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structLocalSettleData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structLocalSettleData.xhtml -> ../html-full/structLocalSettleData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ResetHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ResetHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ResetHandler-members.xhtml -> ../html-full/classgmx_1_1ResetHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineModuleSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineModuleSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineModuleSettings-members.xhtml -> ../html-full/classgmx_1_1CommandLineModuleSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdrunoptions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdrunoptions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdrunoptions_8h__incl.svg -> ../html-full/mdrunoptions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1RefDataFilenameMaker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1RefDataFilenameMaker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1RefDataFilenameMaker-members.xhtml -> ../html-full/classgmx_1_1test_1_1RefDataFilenameMaker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2a7e973503d881e60df68eed40a2f16a.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_2a7e973503d881e60df68eed40a2f16a.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2a7e973503d881e60df68eed40a2f16a.xhtml -> ../html-full/dir_2a7e973503d881e60df68eed40a2f16a.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000052.xhtml -> ../html-full/dir_000111_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/expfit_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/expfit_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/expfit_8h__incl.svg -> ../html-full/expfit_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointData.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointData.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointData.xhtml -> ../html-full/classgmx_1_1CheckpointData.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream-members.xhtml -> ../html-full/classgmx_1_1StringOutputStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetForceSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000100_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000100_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000100_000170.xhtml -> ../html-full/dir_000100_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CpuInfo_1_1LogicalProcessor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CpuInfo_1_1LogicalProcessor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CpuInfo_1_1LogicalProcessor-members.xhtml -> ../html-full/structgmx_1_1CpuInfo_1_1LogicalProcessor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_41_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_50_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_41_dark.png -> ../html-full/form_50_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraitsBase.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraitsBase.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraitsBase.xhtml -> ../html-full/structgmx_1_1OpenClTraitsBase.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structDeviceInformation-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation-members.xhtml -> ../html-full/structDeviceInformation-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AlignedAllocationPolicy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AlignedAllocationPolicy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AlignedAllocationPolicy-members.xhtml -> ../html-full/classgmx_1_1AlignedAllocationPolicy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsBehavior-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsBehavior-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsBehavior-members.xhtml -> ../html-full/classgmx_1_1IOptionsBehavior-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml -> ../html-full/dir_8c6de95273a4a1ab66e54094731e47f5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MappedUnionFinder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MappedUnionFinder-members.xhtml -> ../html-full/classgmx_1_1MappedUnionFinder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/directoryenumerator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/directoryenumerator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/directoryenumerator_8h__incl.svg -> ../html-full/directoryenumerator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineoptionsmodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineoptionsmodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineoptionsmodule_8h__incl.svg -> ../html-full/cmdlineoptionsmodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1gmx__cache__protect__t.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1gmx__cache__protect__t.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1gmx__cache__protect__t.xhtml -> ../html-full/structgmx_1_1gmx__cache__protect__t.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceOutputs-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceOutputs-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceOutputs-members.xhtml -> ../html-full/classgmx_1_1ForceOutputs-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_nbnxm.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/page_nbnxm.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/page_nbnxm.xhtml -> ../html-full/page_nbnxm.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Numa-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Numa-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Numa-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Numa-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSetManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LocalAtomSetManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LocalAtomSetManager-members.xhtml -> ../html-full/classgmx_1_1LocalAtomSetManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__kernel__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hip__kernel__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__kernel__utils_8h__incl.svg -> ../html-full/hip__kernel__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7156828c8d148b9c7ab68f09210221be.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7156828c8d148b9c7ab68f09210221be.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7156828c8d148b9c7ab68f09210221be.xhtml -> ../html-full/dir_7156828c8d148b9c7ab68f09210221be.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_13.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_13.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_13.svg -> ../html-full/msc_inline_mscgraph_13.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EqualCaseInsensitive.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EqualCaseInsensitive.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EqualCaseInsensitive.xhtml -> ../html-full/classgmx_1_1EqualCaseInsensitive.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileOptions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DataFileOptions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DataFileOptions-members.xhtml -> ../html-full/classgmx_1_1DataFileOptions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlumedInputFilename.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PlumedInputFilename.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlumedInputFilename.xhtml -> ../html-full/structgmx_1_1PlumedInputFilename.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CompileTimeStringJoin-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CompileTimeStringJoin-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CompileTimeStringJoin-members.xhtml -> ../html-full/structgmx_1_1CompileTimeStringJoin-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/path_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/path_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/path_8h__incl.svg -> ../html-full/path_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsIterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsIterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsIterator-members.xhtml -> ../html-full/classgmx_1_1OptionsIterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/builder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/builder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/builder_8h__incl.svg -> ../html-full/builder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AffineTransformation-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AffineTransformation-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AffineTransformation-members.xhtml -> ../html-full/classgmx_1_1AffineTransformation-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForceHelperBuffers-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForceHelperBuffers-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classForceHelperBuffers-members.xhtml -> ../html-full/classForceHelperBuffers-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000053_000028.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000053_000028.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000053_000028.xhtml -> ../html-full/dir_000053_000028.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDModulesNotifier-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDModulesNotifier-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDModulesNotifier-members.xhtml -> ../html-full/classgmx_1_1MDModulesNotifier-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1TextFileMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_41.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_50.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_41.png -> ../html-full/form_50.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32474fd9548d0f2ad92adb149653ad10.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_32474fd9548d0f2ad92adb149653ad10.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32474fd9548d0f2ad92adb149653ad10.xhtml -> ../html-full/dir_32474fd9548d0f2ad92adb149653ad10.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testmatchers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testmatchers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testmatchers_8h__incl.svg -> ../html-full/testmatchers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml -> ../html-full/dir_34dd9222320d41e3c3d43a608989ea3b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape-members.xhtml -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_3d58593a3fd598cc22f8788b7ddedf2e.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_3d58593a3fd598cc22f8788b7ddedf2e.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_3d58593a3fd598cc22f8788b7ddedf2e.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant_3_01Enum_00_01typename_01std_1_1enable__if__t_3_3d58593a3fd598cc22f8788b7ddedf2e.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000162.xhtml -> ../html-full/dir_000023_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pmalloc_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pmalloc_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pmalloc_8h__incl.svg -> ../html-full/pmalloc_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorConfig-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulatorConfig-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulatorConfig-members.xhtml -> ../html-full/structgmx_1_1SimulatorConfig-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_af3696197bf82a93bf282a2e5bb38332.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_af3696197bf82a93bf282a2e5bb38332.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_af3696197bf82a93bf282a2e5bb38332.xhtml -> ../html-full/dir_af3696197bf82a93bf282a2e5bb38332.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9223769e7949ef0e535eb89ee496ca73.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9223769e7949ef0e535eb89ee496ca73.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9223769e7949ef0e535eb89ee496ca73.xhtml -> ../html-full/dir_9223769e7949ef0e535eb89ee496ca73.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ac0c8b41ed0200ca73ac5d4028c90ed3.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ac0c8b41ed0200ca73ac5d4028c90ed3.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ac0c8b41ed0200ca73ac5d4028c90ed3.xhtml -> ../html-full/dir_ac0c8b41ed0200ca73ac5d4028c90ed3.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09141f8584d4385ef272b4a84e5b3373.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_09141f8584d4385ef272b4a84e5b3373.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09141f8584d4385ef272b4a84e5b3373.xhtml -> ../html-full/dir_09141f8584d4385ef272b4a84e5b3373.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d01c07398b4254f96a7150c96b79b270.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_d01c07398b4254f96a7150c96b79b270.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d01c07398b4254f96a7150c96b79b270.xhtml -> ../html-full/dir_d01c07398b4254f96a7150c96b79b270.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoOptionalOutput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1NoOptionalOutput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NumericalSplineTableInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput-members.xhtml -> ../html-full/structgmx_1_1NumericalSplineTableInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5cdafd7241d2493bf10eba16c24df27.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a5cdafd7241d2493bf10eba16c24df27.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5cdafd7241d2493bf10eba16c24df27.xhtml -> ../html-full/dir_a5cdafd7241d2493bf10eba16c24df27.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_15_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_15_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_15_dark.png -> ../html-full/form_15_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml -> ../html-full/dir_722cc9c213a4257cb0b17841f3a71d25.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e6ddf929e6679f18ebcc713bf7c5cec.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1e6ddf929e6679f18ebcc713bf7c5cec.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1e6ddf929e6679f18ebcc713bf7c5cec.xhtml -> ../html-full/dir_1e6ddf929e6679f18ebcc713bf7c5cec.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData-members.xhtml -> ../html-full/classgmx_1_1PotentialPointData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionValueConverterSimple-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionValueConverterSimple-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionValueConverterSimple-members.xhtml -> ../html-full/classgmx_1_1OptionValueConverterSimple-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpp__atomtype_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpp__atomtype_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpp__atomtype_8h__incl.svg -> ../html-full/gpp__atomtype_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IKeyValueTreeTransformRules-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IKeyValueTreeTransformRules-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IKeyValueTreeTransformRules-members.xhtml -> ../html-full/classgmx_1_1IKeyValueTreeTransformRules-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000157_000028.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000157_000028.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000157_000028.xhtml -> ../html-full/dir_000157_000028.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConstraintsParam-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConstraintsParam-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConstraintsParam-members.xhtml -> ../html-full/classgmx_1_1ConstraintsParam-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_10_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_10_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_10_dark.png -> ../html-full/form_10_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structFEPStateValue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structFEPStateValue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structFEPStateValue-members.xhtml -> ../html-full/structFEPStateValue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1nbnxn__cycle__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1nbnxn__cycle__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1nbnxn__cycle__t-members.xhtml -> ../html-full/classgmx_1_1nbnxn__cycle__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesAtomsRedistributedSignal-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal-members.xhtml -> ../html-full/structgmx_1_1MDModulesAtomsRedistributedSignal-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_29_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_31_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_29_dark.png -> ../html-full/form_31_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpLinks-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1HelpLinks-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1HelpLinks-members.xhtml -> ../html-full/classgmx_1_1HelpLinks-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSectionHandle__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MdRunInputFilename.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MdRunInputFilename.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MdRunInputFilename.xhtml -> ../html-full/structgmx_1_1MdRunInputFilename.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EdrOutputFilename.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EdrOutputFilename.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EdrOutputFilename.xhtml -> ../html-full/structgmx_1_1EdrOutputFilename.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListIterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListIterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListIterator-members.xhtml -> ../html-full/classIListIterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BuildMDModulesNotifier_3_01CurrentCallParameter_00_01CallParameter_8_8_8_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BuildMDModulesNotifier_3_01CurrentCallParameter_00_01CallParameter_8_8_8_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BuildMDModulesNotifier_3_01CurrentCallParameter_00_01CallParameter_8_8_8_01_4-members.xhtml -> ../html-full/structgmx_1_1BuildMDModulesNotifier_3_01CurrentCallParameter_00_01CallParameter_8_8_8_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_96ab0e0c3487cfe17417b7953707b649.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_96ab0e0c3487cfe17417b7953707b649.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_96ab0e0c3487cfe17417b7953707b649.xhtml -> ../html-full/dir_96ab0e0c3487cfe17417b7953707b649.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UnionFinder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UnionFinder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UnionFinder-members.xhtml -> ../html-full/classgmx_1_1UnionFinder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml -> ../html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomIterator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomIterator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomIterator-members.xhtml -> ../html-full/classAtomIterator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringutil_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringutil_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringutil_8h__incl.svg -> ../html-full/stringutil_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_29.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_31.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_29.png -> ../html-full/form_31.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingVisitor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingVisitor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingVisitor-members.xhtml -> ../html-full/classgmx_1_1OptionsModifyingVisitor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulationTimeStep.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulationTimeStep.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulationTimeStep.xhtml -> ../html-full/structgmx_1_1SimulationTimeStep.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenm_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filenm_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filenm_8h__incl.svg -> ../html-full/filenm_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DataFileInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DataFileInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DataFileInfo-members.xhtml -> ../html-full/structgmx_1_1DataFileInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2.xhtml -> ../html-full/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textreader_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textreader_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textreader_8h__incl.svg -> ../html-full/textreader_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TopologyData-members.xhtml -> ../html-full/classgmx_1_1TopologyData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMDOutputProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IMDOutputProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IMDOutputProvider-members.xhtml -> ../html-full/classgmx_1_1IMDOutputProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/displacement_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/displacement_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/displacement_8h__incl.svg -> ../html-full/displacement_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_29f1a674ba1859f41704372482980b85.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85.xhtml -> ../html-full/dir_29f1a674ba1859f41704372482980b85.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculePatchDatabase-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase-members.xhtml -> ../html-full/structMoleculePatchDatabase-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignal-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationSignal-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationSignal-members.xhtml -> ../html-full/classgmx_1_1SimulationSignal-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000062_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000062_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000062_000169.xhtml -> ../html-full/dir_000062_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomentum-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomentum-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomentum-members.xhtml -> ../html-full/structSystemMomentum-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GlobalCommandLineHelpContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GlobalCommandLineHelpContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GlobalCommandLineHelpContext-members.xhtml -> ../html-full/classgmx_1_1GlobalCommandLineHelpContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MrcDensityMapOfFloatWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MrcDensityMapOfFloatWriter-members.xhtml -> ../html-full/classgmx_1_1MrcDensityMapOfFloatWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c428f345b527d2071b666c6f8374398.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c428f345b527d2071b666c6f8374398.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c428f345b527d2071b666c6f8374398.xhtml -> ../html-full/dir_8c428f345b527d2071b666c6f8374398.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1StdioTestHelper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1StdioTestHelper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1StdioTestHelper-members.xhtml -> ../html-full/classgmx_1_1test_1_1StdioTestHelper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringContext-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MessageStringContext-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MessageStringContext-members.xhtml -> ../html-full/classgmx_1_1MessageStringContext-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataParallelOptions-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataParallelOptions-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataParallelOptions-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataParallelOptions-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000144_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000144_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000144_000002.xhtml -> ../html-full/dir_000144_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IExecutableEnvironment-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IExecutableEnvironment-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IExecutableEnvironment-members.xhtml -> ../html-full/classgmx_1_1IExecutableEnvironment-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CoordinatesAndBoxPreprocessed-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed-members.xhtml -> ../html-full/structgmx_1_1CoordinatesAndBoxPreprocessed-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_14_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_14_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_14_dark.png -> ../html-full/form_14_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFileOutputRedirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFileOutputRedirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFileOutputRedirector-members.xhtml -> ../html-full/classgmx_1_1IFileOutputRedirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDataStatistics-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDataStatistics-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDataStatistics-members.xhtml -> ../html-full/structgmx_1_1MrcDataStatistics-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Profiling-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Profiling-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Profiling-members.xhtml -> ../html-full/classgmx_1_1Profiling-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structAtomsAdjacencyListElement-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structAtomsAdjacencyListElement-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structAtomsAdjacencyListElement-members.xhtml -> ../html-full/structAtomsAdjacencyListElement-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_38_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_40_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_38_dark.png -> ../html-full/form_40_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_10.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_10.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_10.png -> ../html-full/form_10.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/manyautocorrelation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/manyautocorrelation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/manyautocorrelation_8h__incl.svg -> ../html-full/manyautocorrelation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuTaskAssignmentsBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GpuTaskAssignmentsBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1GpuTaskAssignmentsBuilder-members.xhtml -> ../html-full/classgmx_1_1GpuTaskAssignmentsBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_15.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_15.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_15.png -> ../html-full/form_15.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDeviceStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classDeviceStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classDeviceStream-members.xhtml -> ../html-full/classDeviceStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BoolType-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BoolType-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BoolType-members.xhtml -> ../html-full/structgmx_1_1BoolType-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringToEnumValueConverter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringToEnumValueConverter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringToEnumValueConverter-members.xhtml -> ../html-full/classgmx_1_1StringToEnumValueConverter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1NumaNode-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1NumaNode-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1NumaNode-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1NumaNode-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_14.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_14.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_14.png -> ../html-full/form_14.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude-members.xhtml -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1layout__right.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1layout__right.xhtml -> ../html-full/classgmx_1_1layout__right.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ITopologyProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ITopologyProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ITopologyProvider-members.xhtml -> ../html-full/classgmx_1_1ITopologyProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsVisitor-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsVisitor-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsVisitor-members.xhtml -> ../html-full/classgmx_1_1OptionsVisitor-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1beec4451a575fca81beb42517047512.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1beec4451a575fca81beb42517047512.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1beec4451a575fca81beb42517047512.xhtml -> ../html-full/dir_1beec4451a575fca81beb42517047512.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__sparsematrix-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__sparsematrix-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__sparsematrix-members.xhtml -> ../html-full/structgmx__sparsematrix-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WriteCheckpointDataHolder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1WriteCheckpointDataHolder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1WriteCheckpointDataHolder-members.xhtml -> ../html-full/classgmx_1_1WriteCheckpointDataHolder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b0856f6b0d80ccb263b2f415c91f9e17.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b0856f6b0d80ccb263b2f415c91f9e17.xhtml -> ../html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopHandler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StopHandler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopHandler-members.xhtml -> ../html-full/classgmx_1_1StopHandler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa16baa95be1082e33976e526f10737d.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_fa16baa95be1082e33976e526f10737d.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_fa16baa95be1082e33976e526f10737d.xhtml -> ../html-full/dir_fa16baa95be1082e33976e526f10737d.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000041_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000041_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000041_000002.xhtml -> ../html-full/dir_000041_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ee8b3903a5b832a547d4c24143fdba12.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_ee8b3903a5b832a547d4c24143fdba12.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_ee8b3903a5b832a547d4c24143fdba12.xhtml -> ../html-full/dir_ee8b3903a5b832a547d4c24143fdba12.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryFileOpener-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryFileOpener-members.xhtml -> ../html-full/classgmx_1_1TrajectoryFileOpener-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream-members.xhtml -> ../html-full/classgmx_1_1TextOutputStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SeparatePmeRanksPermitted-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SeparatePmeRanksPermitted-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SeparatePmeRanksPermitted-members.xhtml -> ../html-full/classgmx_1_1SeparatePmeRanksPermitted-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExponentialMovingAverageState-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1ExponentialMovingAverageState-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExponentialMovingAverageState-members.xhtml -> ../html-full/structgmx_1_1ExponentialMovingAverageState-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1InstallationPrefixInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1InstallationPrefixInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1InstallationPrefixInfo-members.xhtml -> ../html-full/structgmx_1_1InstallationPrefixInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Core-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Core-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Core-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Core-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputStream-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream-members.xhtml -> ../html-full/classgmx_1_1TextInputStream-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml -> ../html-full/classgmx_1_1NonbondedBenchmarkInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractPlotModule__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000068_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000063.xhtml -> ../html-full/dir_000068_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogLevelHelper-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LogLevelHelper-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LogLevelHelper-members.xhtml -> ../html-full/classgmx_1_1LogLevelHelper-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_u.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_u.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_u.xhtml -> ../html-full/namespacemembers_func_u.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcherSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ITextBlockMatcherSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcherSettings-members.xhtml -> ../html-full/classgmx_1_1test_1_1ITextBlockMatcherSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__ilist-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__ilist-members.xhtml -> ../html-full/structt__ilist-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/output_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/output_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/output_8h__incl.svg -> ../html-full/output_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000137_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000137_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000137_000170.xhtml -> ../html-full/dir_000137_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000041_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000041_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000041_000170.xhtml -> ../html-full/dir_000041_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderOutput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderOutput-members.xhtml -> ../html-full/classgmx_1_1ForceProviderOutput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000096_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000096_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000096_000002.xhtml -> ../html-full/dir_000096_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AnalyticalSplineTableInput-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AnalyticalSplineTableInput-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AnalyticalSplineTableInput-members.xhtml -> ../html-full/structgmx_1_1AnalyticalSplineTableInput-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4-members.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopHandlerBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StopHandlerBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopHandlerBuilder-members.xhtml -> ../html-full/classgmx_1_1StopHandlerBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000096.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000101_000096.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000096.xhtml -> ../html-full/dir_000101_000096.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestOptionsProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestOptionsProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestOptionsProvider-members.xhtml -> ../html-full/classgmx_1_1test_1_1TestOptionsProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DevelopmentFeatureFlags-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DevelopmentFeatureFlags-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DevelopmentFeatureFlags-members.xhtml -> ../html-full/structgmx_1_1DevelopmentFeatureFlags-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CrystallographicLabels-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CrystallographicLabels-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CrystallographicLabels-members.xhtml -> ../html-full/structgmx_1_1CrystallographicLabels-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5a4b6336a2508428a9c6c3ca575d531_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a5a4b6336a2508428a9c6c3ca575d531_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a5a4b6336a2508428a9c6c3ca575d531_dep.svg -> ../html-full/dir_a5a4b6336a2508428a9c6c3ca575d531_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classhistory__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classhistory__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classhistory__t-members.xhtml -> ../html-full/classhistory__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000082.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000097_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000082.xhtml -> ../html-full/dir_000097_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1beec4451a575fca81beb42517047512_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1beec4451a575fca81beb42517047512_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1beec4451a575fca81beb42517047512_dep.svg -> ../html-full/dir_1beec4451a575fca81beb42517047512_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b663cc641e6b1e7a361f6c7cc2d37d1b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b663cc641e6b1e7a361f6c7cc2d37d1b_dep.svg -> ../html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator_3_01false_00_01true_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1PrefixFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1PrefixFormatter-members.xhtml -> ../html-full/structgmx_1_1test_1_1PrefixFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__packed__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09141f8584d4385ef272b4a84e5b3373_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_09141f8584d4385ef272b4a84e5b3373_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_09141f8584d4385ef272b4a84e5b3373_dep.svg -> ../html-full/dir_09141f8584d4385ef272b4a84e5b3373_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml -> ../html-full/dir_1871851d9cfb65be92ceb250f0610eb5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DefaultInitializationAllocator-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DefaultInitializationAllocator-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DefaultInitializationAllocator-members.xhtml -> ../html-full/classgmx_1_1DefaultInitializationAllocator-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000101_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000170.xhtml -> ../html-full/dir_000101_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcherSettings-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1IFileMatcherSettings-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcherSettings-members.xhtml -> ../html-full/classgmx_1_1test_1_1IFileMatcherSettings-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_38.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_40.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_38.png -> ../html-full/form_40.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_22dfbea999db116fd1efebf9609d6e70_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_22dfbea999db116fd1efebf9609d6e70_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_22dfbea999db116fd1efebf9609d6e70_dep.svg -> ../html-full/dir_22dfbea999db116fd1efebf9609d6e70_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000033_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000033_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000033_000170.xhtml -> ../html-full/dir_000033_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClfftInitializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ClfftInitializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ClfftInitializer-members.xhtml -> ../html-full/classgmx_1_1ClfftInitializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesNotifiers-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesNotifiers-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesNotifiers-members.xhtml -> ../html-full/structgmx_1_1MDModulesNotifiers-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConvertTprInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConvertTprInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ConvertTprInfo-members.xhtml -> ../html-full/classgmx_1_1ConvertTprInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__excl__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__excl__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__excl__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__excl__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1ExactTextMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_722cc9c213a4257cb0b17841f3a71d25_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_722cc9c213a4257cb0b17841f3a71d25_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_722cc9c213a4257cb0b17841f3a71d25_dep.svg -> ../html-full/dir_722cc9c213a4257cb0b17841f3a71d25_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__filenm-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__filenm-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__filenm-members.xhtml -> ../html-full/structt__filenm-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9223769e7949ef0e535eb89ee496ca73_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9223769e7949ef0e535eb89ee496ca73_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9223769e7949ef0e535eb89ee496ca73_dep.svg -> ../html-full/dir_9223769e7949ef0e535eb89ee496ca73_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcher-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ITextBlockMatcher-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ITextBlockMatcher-members.xhtml -> ../html-full/classgmx_1_1test_1_1ITextBlockMatcher-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1NoContentsMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000061_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000162.xhtml -> ../html-full/dir_000061_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__im__ei__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__im__ei__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000047_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000047_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000047_000170.xhtml -> ../html-full/dir_000047_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch-members.xhtml -> ../html-full/classgmx_1_1test_1_1NoTextMatch-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359263c2dab7d54b02095b59735995d5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_359263c2dab7d54b02095b59735995d5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359263c2dab7d54b02095b59735995d5_dep.svg -> ../html-full/dir_359263c2dab7d54b02095b59735995d5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000068_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000156.xhtml -> ../html-full/dir_000068_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1isIntegralConstant.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1isIntegralConstant.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1isIntegralConstant.xhtml -> ../html-full/structgmx_1_1isIntegralConstant.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSimulationGroups-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups-members.xhtml -> ../html-full/structSimulationGroups-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> ../html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000170.xhtml -> ../html-full/dir_000059_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000108_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000170.xhtml -> ../html-full/dir_000108_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/broadcaststructs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/broadcaststructs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/broadcaststructs_8h__incl.svg -> ../html-full/broadcaststructs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000162.xhtml -> ../html-full/dir_000160_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Double-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double-members.xhtml -> ../html-full/classgmx_1_1Simd4Double-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000063.xhtml -> ../html-full/dir_000025_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensitySkewData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDensitySkewData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensitySkewData-members.xhtml -> ../html-full/structgmx_1_1MrcDensitySkewData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000162.xhtml -> ../html-full/dir_000021_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000162.xhtml -> ../html-full/dir_000090_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDInt32-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32-members.xhtml -> ../html-full/classgmx_1_1SimdDInt32-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFInt32-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32-members.xhtml -> ../html-full/classgmx_1_1SimdFInt32-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrunutility.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__mdrunutility.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrunutility.svg -> ../html-full/group__module__mdrunutility.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000066_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000162.xhtml -> ../html-full/dir_000066_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__nodecomm__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t-members.xhtml -> ../html-full/structgmx__nodecomm__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDouble-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble-members.xhtml -> ../html-full/classgmx_1_1SimdDouble-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Float-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float-members.xhtml -> ../html-full/classgmx_1_1Simd4Float-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDIBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool-members.xhtml -> ../html-full/classgmx_1_1SimdDIBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4DBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool-members.xhtml -> ../html-full/classgmx_1_1Simd4DBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4FBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool-members.xhtml -> ../html-full/classgmx_1_1Simd4FBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFIBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFIBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFIBool-members.xhtml -> ../html-full/classgmx_1_1SimdFIBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000090.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000090.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000090.xhtml -> ../html-full/dir_000025_000090.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000063.xhtml -> ../html-full/dir_000090_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TprAndFileManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TprAndFileManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TprAndFileManager-members.xhtml -> ../html-full/classgmx_1_1test_1_1TprAndFileManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000158.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000158.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000158.xhtml -> ../html-full/dir_000065_000158.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFloat-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat-members.xhtml -> ../html-full/classgmx_1_1SimdFloat-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFBool-members.xhtml -> ../html-full/classgmx_1_1SimdFBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDBool-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDBool-members.xhtml -> ../html-full/classgmx_1_1SimdDBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcher-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1IFileMatcher-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcher-members.xhtml -> ../html-full/classgmx_1_1test_1_1IFileMatcher-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeGpuProgram-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classPmeGpuProgram-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classPmeGpuProgram-members.xhtml -> ../html-full/classPmeGpuProgram-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000034_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000170.xhtml -> ../html-full/dir_000034_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000100.xhtml -> ../html-full/dir_000087_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1ProcessingUnit-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1ProcessingUnit-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1ProcessingUnit-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1ProcessingUnit-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atomsbuilder_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/atomsbuilder_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atomsbuilder_8h__incl.svg -> ../html-full/atomsbuilder_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFileInputRedirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFileInputRedirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFileInputRedirector-members.xhtml -> ../html-full/classgmx_1_1IFileInputRedirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4-members.xhtml -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSettleWaterTopology-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology-members.xhtml -> ../html-full/structSettleWaterTopology-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000156.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000156.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000156.xhtml -> ../html-full/dir_000135_000156.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml -> ../html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GromppMtsOpts-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GromppMtsOpts-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GromppMtsOpts-members.xhtml -> ../html-full/structgmx_1_1GromppMtsOpts-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml -> ../html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlanSetupData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PlanSetupData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlanSetupData-members.xhtml -> ../html-full/structgmx_1_1PlanSetupData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000048_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000170.xhtml -> ../html-full/dir_000048_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pairs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pairs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pairs_8h__incl.svg -> ../html-full/pairs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000031_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000100.xhtml -> ../html-full/dir_000031_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PullCoordExpressionParser-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PullCoordExpressionParser-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PullCoordExpressionParser-members.xhtml -> ../html-full/classgmx_1_1PullCoordExpressionParser-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_56293306df9b62cfc470e5d2417454ba.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_56293306df9b62cfc470e5d2417454ba.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_56293306df9b62cfc470e5d2417454ba.xhtml -> ../html-full/dir_56293306df9b62cfc470e5d2417454ba.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml -> ../html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml -> ../html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1IEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1IEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1IEntry-members.xhtml -> ../html-full/structt__nblist_1_1IEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingBroadcast-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesCheckpointReadingBroadcast-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingBroadcast-members.xhtml -> ../html-full/structgmx_1_1MDModulesCheckpointReadingBroadcast-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IForceProvider-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IForceProvider-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IForceProvider-members.xhtml -> ../html-full/classgmx_1_1IForceProvider-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__molblock__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__molblock__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__molblock__t-members.xhtml -> ../html-full/structgmx__molblock__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringstream_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringstream_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringstream_8h__incl.svg -> ../html-full/stringstream_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000100.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000045_000100.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000100.xhtml -> ../html-full/dir_000045_000100.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__general_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/impl__reference__general_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/impl__reference__general_8h__incl.svg -> ../html-full/impl__reference__general_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000095_000014.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000095_000014.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000095_000014.xhtml -> ../html-full/dir_000095_000014.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4-members.xhtml -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4-members.xhtml -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputRequirementOptionDirector-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputRequirementOptionDirector-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputRequirementOptionDirector-members.xhtml -> ../html-full/classgmx_1_1OutputRequirementOptionDirector-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000054_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000052.xhtml -> ../html-full/dir_000054_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__hip_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__event__hip_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__event__hip_8h__incl.svg -> ../html-full/device__event__hip_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4-members.xhtml -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/orires_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/orires_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/orires_8h__incl.svg -> ../html-full/orires_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Package-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Package-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Package-members.xhtml -> ../html-full/structgmx_1_1HardwareTopology_1_1Package-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000061.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000061.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000061.xhtml -> ../html-full/dir_000023_000061.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000164_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000164_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000164_000169.xhtml -> ../html-full/dir_000164_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/topologyinformation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/topologyinformation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/topologyinformation_8h__incl.svg -> ../html-full/topologyinformation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_4.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_4.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_4.png -> ../html-full/form_4.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1IsTuple_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1IsTuple_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1IsTuple_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1IsTuple_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_01_4.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryFrameWriter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryFrameWriter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TrajectoryFrameWriter-members.xhtml -> ../html-full/classgmx_1_1TrajectoryFrameWriter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6db5db4c493eb96fab49e5d6350ca481.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6db5db4c493eb96fab49e5d6350ca481.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6db5db4c493eb96fab49e5d6350ca481.xhtml -> ../html-full/dir_6db5db4c493eb96fab49e5d6350ca481.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000022_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000022_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000022_000002.xhtml -> ../html-full/dir_000022_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_532bf28f355a758c5974bf4170215a92.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_532bf28f355a758c5974bf4170215a92.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_532bf28f355a758c5974bf4170215a92.xhtml -> ../html-full/dir_532bf28f355a758c5974bf4170215a92.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopConditionTime-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StopConditionTime-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopConditionTime-members.xhtml -> ../html-full/classgmx_1_1StopConditionTime-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DensityFittingModuleInfo-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DensityFittingModuleInfo-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DensityFittingModuleInfo-members.xhtml -> ../html-full/structgmx_1_1DensityFittingModuleInfo-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classEwaldBoxZScaler-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classEwaldBoxZScaler-members.xhtml -> ../html-full/classEwaldBoxZScaler-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000085_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000085_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000085_000169.xhtml -> ../html-full/dir_000085_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringCompare-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringCompare-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringCompare-members.xhtml -> ../html-full/classgmx_1_1StringCompare-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringFormatter-members.xhtml -> ../html-full/classgmx_1_1StringFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3706a2088846aeea3bf8dc88b1a89878.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3706a2088846aeea3bf8dc88b1a89878.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3706a2088846aeea3bf8dc88b1a89878.xhtml -> ../html-full/dir_3706a2088846aeea3bf8dc88b1a89878.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml -> ../html-full/dir_a404b2cbf9db2e547ba9696baa2a562b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnsembleTemperature-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnsembleTemperature-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnsembleTemperature-members.xhtml -> ../html-full/structgmx_1_1EnsembleTemperature-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7e013631519469366ffd6bf609372539.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7e013631519469366ffd6bf609372539.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7e013631519469366ffd6bf609372539.xhtml -> ../html-full/dir_7e013631519469366ffd6bf609372539.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml -> ../html-full/dir_b663cc641e6b1e7a361f6c7cc2d37d1b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b6e3abb9460d35a8114626fa31e62381.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b6e3abb9460d35a8114626fa31e62381.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b6e3abb9460d35a8114626fa31e62381.xhtml -> ../html-full/dir_b6e3abb9460d35a8114626fa31e62381.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359263c2dab7d54b02095b59735995d5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_359263c2dab7d54b02095b59735995d5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359263c2dab7d54b02095b59735995d5.xhtml -> ../html-full/dir_359263c2dab7d54b02095b59735995d5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopConditionSignal-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StopConditionSignal-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StopConditionSignal-members.xhtml -> ../html-full/classgmx_1_1StopConditionSignal-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator__impl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/alignedallocator__impl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/alignedallocator__impl_8h__incl.svg -> ../html-full/alignedallocator__impl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml -> ../html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_35311b9bd028366f3a4c4732c958bfe5.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5.xhtml -> ../html-full/dir_35311b9bd028366f3a4c4732c958bfe5.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_22dfbea999db116fd1efebf9609d6e70.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_22dfbea999db116fd1efebf9609d6e70.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_22dfbea999db116fd1efebf9609d6e70.xhtml -> ../html-full/dir_22dfbea999db116fd1efebf9609d6e70.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3d71ad7d27d849c1edfa7e85354eafed.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3d71ad7d27d849c1edfa7e85354eafed.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3d71ad7d27d849c1edfa7e85354eafed.xhtml -> ../html-full/dir_3d71ad7d27d849c1edfa7e85354eafed.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle-members.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000063.xhtml -> ../html-full/dir_000111_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pointers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pointers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pointers_8h__incl.svg -> ../html-full/pointers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structReplicaExchangeParameters-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structReplicaExchangeParameters-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structReplicaExchangeParameters-members.xhtml -> ../html-full/structReplicaExchangeParameters-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_4_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_4_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_4_dark.png -> ../html-full/form_4_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPartialDeserializedTprFile-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile-members.xhtml -> ../html-full/structPartialDeserializedTprFile-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RocfftInitializer-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RocfftInitializer-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RocfftInitializer-members.xhtml -> ../html-full/classgmx_1_1RocfftInitializer-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1FormatterVariant-members.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1FormatterVariant-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000009_000083.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000083.xhtml -> ../html-full/dir_000009_000083.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_2.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_2.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_2.png -> ../html-full/form_2.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTableBuilder-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classStringTableBuilder-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classStringTableBuilder-members.xhtml -> ../html-full/classStringTableBuilder-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InteractiveMD-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InteractiveMD-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InteractiveMD-members.xhtml -> ../html-full/classgmx_1_1InteractiveMD-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1IsTuple.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1IsTuple.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1IsTuple.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1IsTuple.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_3_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_3_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_3_dark.png -> ../html-full/form_3_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ILogTarget-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ILogTarget-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ILogTarget-members.xhtml -> ../html-full/classgmx_1_1ILogTarget-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__ewald.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__ewald.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__ewald.svg -> ../html-full/group__module__ewald.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_3.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_3.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_3.png -> ../html-full/form_3.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000093.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000093.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000093.xhtml -> ../html-full/dir_000160_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000052.xhtml -> ../html-full/dir_000059_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000041.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000101_000041.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000101_000041.xhtml -> ../html-full/dir_000101_000041.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomRange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAtomRange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classAtomRange-members.xhtml -> ../html-full/classAtomRange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000108_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000108_000018.xhtml -> ../html-full/dir_000108_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000007.xhtml -> ../html-full/dir_000065_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000120_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000170.xhtml -> ../html-full/dir_000120_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000074_000082.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000074_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000074_000082.xhtml -> ../html-full/dir_000074_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000026.xhtml -> ../html-full/dir_000087_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListRange-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListRange-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListRange-members.xhtml -> ../html-full/classIListRange-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker-members.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToDensityFittingRequestChecker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000008.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000008.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000008.xhtml -> ../html-full/dir_000065_000008.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000009_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000170.xhtml -> ../html-full/dir_000009_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000074_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000074_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000074_000169.xhtml -> ../html-full/dir_000074_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants.xhtml -> ../html-full/structgmx_1_1test_1_1detail_1_1ParamsToFormatterVariants.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExclusionBlock-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1ExclusionBlock-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1ExclusionBlock-members.xhtml -> ../html-full/structgmx_1_1ExclusionBlock-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_5_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_5_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_5_dark.png -> ../html-full/form_5_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml -> ../html-full/dir_785d6d0c2c6073a66ffd258f1b901773.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1QMInputFileName-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1QMInputFileName-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1QMInputFileName-members.xhtml -> ../html-full/structgmx_1_1QMInputFileName-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000070_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000070_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000070_000169.xhtml -> ../html-full/dir_000070_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_051edbf3de11cf568168f65483ae264b.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_051edbf3de11cf568168f65483ae264b.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_051edbf3de11cf568168f65483ae264b.xhtml -> ../html-full/dir_051edbf3de11cf568168f65483ae264b.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000146_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000146_000170.xhtml -> ../html-full/dir_000146_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_5.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_5.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_5.png -> ../html-full/form_5.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000120_000083.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000083.xhtml -> ../html-full/dir_000120_000083.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyanalysisframe_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/energyanalysisframe_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyanalysisframe_8h__incl.svg -> ../html-full/energyanalysisframe_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000097.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000097.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000097.xhtml -> ../html-full/dir_000166_000097.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000000_000082.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000000_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000000_000082.xhtml -> ../html-full/dir_000000_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_17cbbc99af1269e66445656231b09878.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_17cbbc99af1269e66445656231b09878.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_17cbbc99af1269e66445656231b09878.xhtml -> ../html-full/dir_17cbbc99af1269e66445656231b09878.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t-members.xhtml -> ../html-full/structgmx__localtop__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000031_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000026.xhtml -> ../html-full/dir_000031_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000019.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000019.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000019.xhtml -> ../html-full/dir_000023_000019.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyhistory_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/energyhistory_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/energyhistory_8h__incl.svg -> ../html-full/energyhistory_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classBalanceRegion-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classBalanceRegion-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classBalanceRegion-members.xhtml -> ../html-full/classBalanceRegion-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_2_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_2_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_2_dark.png -> ../html-full/form_2_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000034_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000034_000018.xhtml -> ../html-full/dir_000034_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IonSwapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IonSwapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IonSwapping-members.xhtml -> ../html-full/classgmx_1_1IonSwapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_51_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42_dark.png -> ../html-full/form_51_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000091_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000091_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000091_000071.xhtml -> ../html-full/dir_000091_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000008.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000171_000008.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000171_000008.xhtml -> ../html-full/dir_000171_000008.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LennardJonesCalculator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LennardJonesCalculator.xhtml -> ../html-full/classgmx_1_1LennardJonesCalculator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HaloMpiRequests-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HaloMpiRequests-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HaloMpiRequests-members.xhtml -> ../html-full/structgmx_1_1HaloMpiRequests-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyNameUnit-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EnergyNameUnit-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EnergyNameUnit-members.xhtml -> ../html-full/structgmx_1_1EnergyNameUnit-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_49e56c817e5e54854c35e136979f97ca.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_49e56c817e5e54854c35e136979f97ca.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_49e56c817e5e54854c35e136979f97ca.xhtml -> ../html-full/dir_49e56c817e5e54854c35e136979f97ca.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml -> ../html-full/classgmx_1_1EnumClassSuitsEnumerationArray-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__index__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__index__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__index__t-members.xhtml -> ../html-full/structgmx__ana__index__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000003.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000003.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000003.xhtml -> ../html-full/dir_000025_000003.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpwritercontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/helpwritercontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpwritercontext_8h__incl.svg -> ../html-full/helpwritercontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GpuTaskMapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GpuTaskMapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GpuTaskMapping-members.xhtml -> ../html-full/structgmx_1_1GpuTaskMapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ga2la__t_1_1Entry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry-members.xhtml -> ../html-full/structgmx__ga2la__t_1_1Entry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000045_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000026.xhtml -> ../html-full/dir_000045_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000048_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000048_000018.xhtml -> ../html-full/dir_000048_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000032_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000032_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000032_000071.xhtml -> ../html-full/dir_000032_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000082.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000082.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000082.xhtml -> ../html-full/dir_000166_000082.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta-members.xhtml -> ../html-full/structSystemMomenta-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000166_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000166_000169.xhtml -> ../html-full/dir_000166_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListProxy-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classIListProxy-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classIListProxy-members.xhtml -> ../html-full/classIListProxy-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__history_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/awh__history_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__history_8h__incl.svg -> ../html-full/awh__history_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000037_000008.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000037_000008.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000037_000008.xhtml -> ../html-full/dir_000037_000008.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintpotential_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/restraintpotential_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintpotential_8h__incl.svg -> ../html-full/restraintpotential_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MrcDensityMapHeader__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MrcDensityMapHeader__coll__graph.svg -> ../html-full/structgmx_1_1MrcDensityMapHeader__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1JEntry-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__nblist_1_1JEntry-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__nblist_1_1JEntry-members.xhtml -> ../html-full/structt__nblist_1_1JEntry-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000052.xhtml -> ../html-full/dir_000087_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker-members.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToNNPotRequestChecker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000086_000026.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000086_000026.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000086_000026.xhtml -> ../html-full/dir_000086_000026.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000065.xhtml -> ../html-full/dir_000017_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000014.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000061_000014.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000014.xhtml -> ../html-full/dir_000061_000014.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000046_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000046_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000046_000071.xhtml -> ../html-full/dir_000046_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__t-members.xhtml -> ../html-full/structgmx_1_1nbnxn__cj__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000051_000008.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000051_000008.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000051_000008.xhtml -> ../html-full/dir_000051_000008.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mpitest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mpitest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mpitest_8h__incl.svg -> ../html-full/mpitest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker-members.xhtml -> ../html-full/structgmx_1_1MDModulesEnergyOutputToQMMMRequestChecker-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/scalar_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar_8h__incl.svg -> ../html-full/scalar_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000103.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000103.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000103.xhtml -> ../html-full/dir_000023_000103.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000162.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000162.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000162.xhtml -> ../html-full/dir_000017_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structWaterMolecule-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structWaterMolecule-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structWaterMolecule-members.xhtml -> ../html-full/structWaterMolecule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/observablesreducer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/observablesreducer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/observablesreducer_8h__incl.svg -> ../html-full/observablesreducer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h__dep__incl.svg -> ../html-full/gpuregiontimer_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000031_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000052.xhtml -> ../html-full/dir_000031_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringtest_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stringtest_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stringtest_8h__incl.svg -> ../html-full/stringtest_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MtsLevel-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MtsLevel-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MtsLevel-members.xhtml -> ../html-full/structgmx_1_1MtsLevel-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000065.xhtml -> ../html-full/dir_000023_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000038.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000068_000038.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000038.xhtml -> ../html-full/dir_000068_000038.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AllocatorTest-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AllocatorTest-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AllocatorTest-members.xhtml -> ../html-full/classgmx_1_1test_1_1AllocatorTest-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000106.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000106.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000106.xhtml -> ../html-full/dir_000065_000106.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpp__bond__atomtype_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpp__bond__atomtype_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpp__bond__atomtype_8h__incl.svg -> ../html-full/gpp__bond__atomtype_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000170_000008.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000170_000008.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000170_000008.xhtml -> ../html-full/dir_000170_000008.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml -> ../html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000107.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000107.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000107.xhtml -> ../html-full/dir_000160_000107.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000007.xhtml -> ../html-full/dir_000090_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AtomPair-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AtomPair-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AtomPair-members.xhtml -> ../html-full/structgmx_1_1AtomPair-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000063.xhtml -> ../html-full/dir_000017_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000165_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000165_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000165_000170.xhtml -> ../html-full/dir_000165_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000045_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000045_000052.xhtml -> ../html-full/dir_000045_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingDataOnMain-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesCheckpointReadingDataOnMain-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesCheckpointReadingDataOnMain-members.xhtml -> ../html-full/structgmx_1_1MDModulesCheckpointReadingDataOnMain-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000077_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000077_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000077_000063.xhtml -> ../html-full/dir_000077_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000072_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000052.xhtml -> ../html-full/dir_000072_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000158.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000158.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000158.xhtml -> ../html-full/dir_000090_000158.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping-members.xhtml -> ../html-full/structt__mapping-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EqualCaseInsensitive-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EqualCaseInsensitive-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EqualCaseInsensitive-members.xhtml -> ../html-full/classgmx_1_1EqualCaseInsensitive-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator.xhtml -> ../html-full/classgmx_1_1CoulombCalculator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000018.xhtml -> ../html-full/dir_000160_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a504950c834d58a27b0bd71a5abd3a11_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a504950c834d58a27b0bd71a5abd3a11_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a504950c834d58a27b0bd71a5abd3a11_dep.svg -> ../html-full/dir_a504950c834d58a27b0bd71a5abd3a11_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_47a33c267ad25ab03f8a184084dc491a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_47a33c267ad25ab03f8a184084dc491a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_47a33c267ad25ab03f8a184084dc491a_dep.svg -> ../html-full/dir_47a33c267ad25ab03f8a184084dc491a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__symbuf-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf-members.xhtml -> ../html-full/structt__symbuf-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000106_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000106_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000106_000063.xhtml -> ../html-full/dir_000106_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000093_000170.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000093_000170.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000093_000170.xhtml -> ../html-full/dir_000093_000170.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structwallcc__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structwallcc__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structwallcc__t-members.xhtml -> ../html-full/structwallcc__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg -> ../html-full/dir_9706143f1a9672f55fea9dcef926a9b9_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1IsSerializableEnum-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1IsSerializableEnum-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1IsSerializableEnum-members.xhtml -> ../html-full/structgmx_1_1IsSerializableEnum-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_114bfa3fdfe57aaaa54acbd4bd7da5c6_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_114bfa3fdfe57aaaa54acbd4bd7da5c6_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_114bfa3fdfe57aaaa54acbd4bd7da5c6_dep.svg -> ../html-full/dir_114bfa3fdfe57aaaa54acbd4bd7da5c6_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5de40b585e9aa7d4c00bdcb37e5b399d_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_5de40b585e9aa7d4c00bdcb37e5b399d_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_5de40b585e9aa7d4c00bdcb37e5b399d_dep.svg -> ../html-full/dir_5de40b585e9aa7d4c00bdcb37e5b399d_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_872b5e52564537be15ead79998acdb8a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_872b5e52564537be15ead79998acdb8a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_872b5e52564537be15ead79998acdb8a_dep.svg -> ../html-full/dir_872b5e52564537be15ead79998acdb8a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000085_000070.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000085_000070.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000085_000070.xhtml -> ../html-full/dir_000085_000070.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000111_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000111_000069.xhtml -> ../html-full/dir_000111_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdDInt32Tag.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimdDInt32Tag.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdDInt32Tag.xhtml -> ../html-full/structgmx_1_1SimdDInt32Tag.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdFInt32Tag.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimdFInt32Tag.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdFInt32Tag.xhtml -> ../html-full/structgmx_1_1SimdFInt32Tag.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b3b10afaa073fb580ca3168487895926_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b3b10afaa073fb580ca3168487895926_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b3b10afaa073fb580ca3168487895926_dep.svg -> ../html-full/dir_b3b10afaa073fb580ca3168487895926_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdDoubleTag.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimdDoubleTag.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdDoubleTag.xhtml -> ../html-full/structgmx_1_1SimdDoubleTag.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e3005fccce81b430ecaf4f4ae7f955ec_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_e3005fccce81b430ecaf4f4ae7f955ec_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_e3005fccce81b430ecaf4f4ae7f955ec_dep.svg -> ../html-full/dir_e3005fccce81b430ecaf4f4ae7f955ec_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_51.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_42.png -> ../html-full/form_51.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_k.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_k.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_k.xhtml -> ../html-full/namespacemembers_k.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4df9e60096d6dee0822ec0bd769c414e_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4df9e60096d6dee0822ec0bd769c414e_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4df9e60096d6dee0822ec0bd769c414e_dep.svg -> ../html-full/dir_4df9e60096d6dee0822ec0bd769c414e_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_32e69e102eaf0237b7d1b4663f024c2e_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e_dep.svg -> ../html-full/dir_32e69e102eaf0237b7d1b4663f024c2e_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000068.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000068.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000068.xhtml -> ../html-full/dir_000025_000068.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdFloatTag.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimdFloatTag.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimdFloatTag.xhtml -> ../html-full/structgmx_1_1SimdFloatTag.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cpuinfo_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cpuinfo_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cpuinfo_8h__incl.svg -> ../html-full/cpuinfo_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesWriteCheckpointData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData-members.xhtml -> ../html-full/structgmx_1_1MDModulesWriteCheckpointData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000022_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000022_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000022_000052.xhtml -> ../html-full/dir_000022_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000022.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000120_000022.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000120_000022.xhtml -> ../html-full/dir_000120_000022.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b1cc3c1f7e4ffa781d72a73ef80cd151_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b1cc3c1f7e4ffa781d72a73ef80cd151_dep.svg -> ../html-full/dir_b1cc3c1f7e4ffa781d72a73ef80cd151_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleTest__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ModuleTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleTest__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1ModuleTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2_dep.svg -> ../html-full/dir_3f4c858b8c7ac8f08dec80d5ddc3a1e2_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_v.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/globals_v.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_v.xhtml -> ../html-full/globals_v.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionManager-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionManager-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionManager-members.xhtml -> ../html-full/classgmx_1_1IOptionManager-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c967dac1b679d5762f622f5d0982f1b6_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c967dac1b679d5762f622f5d0982f1b6_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c967dac1b679d5762f622f5d0982f1b6_dep.svg -> ../html-full/dir_c967dac1b679d5762f622f5d0982f1b6_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000071.xhtml -> ../html-full/dir_000017_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IdentityFormatter-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IdentityFormatter-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IdentityFormatter-members.xhtml -> ../html-full/classgmx_1_1IdentityFormatter-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyAccumulator.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnergyAccumulator.xhtml -> ../html-full/classgmx_1_1EnergyAccumulator.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000068.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000068.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000068.xhtml -> ../html-full/dir_000090_000068.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_010_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml -> ../html-full/structgmx_1_1StaticLog2_3_011_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000071.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000054_000071.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000054_000071.xhtml -> ../html-full/dir_000054_000071.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml -> ../html-full/dir_0188a3e6da905bc60aceb35bf790b8c9.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000068.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000061_000068.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000061_000068.xhtml -> ../html-full/dir_000061_000068.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg -> ../html-full/dir_35311b9bd028366f3a4c4732c958bfe5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraitsBase-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraitsBase-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraitsBase-members.xhtml -> ../html-full/structgmx_1_1OpenClTraitsBase-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_39_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_48_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_39_dark.png -> ../html-full/form_48_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000018.xhtml -> ../html-full/dir_000025_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000014.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000071_000014.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000014.xhtml -> ../html-full/dir_000071_000014.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000066_000083.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000083.xhtml -> ../html-full/dir_000066_000083.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000038.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000135_000038.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000135_000038.xhtml -> ../html-full/dir_000135_000038.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000065.xhtml -> ../html-full/dir_000025_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionListHandle-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structInteractionListHandle-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structInteractionListHandle-members.xhtml -> ../html-full/structInteractionListHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1gmx__cache__protect__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1gmx__cache__protect__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1gmx__cache__protect__t-members.xhtml -> ../html-full/structgmx_1_1gmx__cache__protect__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleParallel__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlumedInputFilename-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PlumedInputFilename-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PlumedInputFilename-members.xhtml -> ../html-full/structgmx_1_1PlumedInputFilename-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteractionList-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structBondedInteractionList-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structBondedInteractionList-members.xhtml -> ../html-full/structBondedInteractionList-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MdRunInputFilename-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MdRunInputFilename-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MdRunInputFilename-members.xhtml -> ../html-full/structgmx_1_1MdRunInputFilename-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1no__delete-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1no__delete-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1no__delete-members.xhtml -> ../html-full/structgmx_1_1no__delete-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits.xhtml -> ../html-full/structgmx_1_1OpenClTraits.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t__coll__graph.svg -> ../html-full/structgmx__localtop__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000069.xhtml -> ../html-full/dir_000065_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EdrOutputFilename-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1EdrOutputFilename-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1EdrOutputFilename-members.xhtml -> ../html-full/structgmx_1_1EdrOutputFilename-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1StaticLog2-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1StaticLog2-members.xhtml -> ../html-full/structgmx_1_1StaticLog2-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulationTimeStep-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1SimulationTimeStep-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1SimulationTimeStep-members.xhtml -> ../html-full/structgmx_1_1SimulationTimeStep-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000003.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000071_000003.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000003.xhtml -> ../html-full/dir_000071_000003.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000003.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000003.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000003.xhtml -> ../html-full/dir_000021_000003.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000144_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000144_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000144_000052.xhtml -> ../html-full/dir_000144_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000066.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000068_000066.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000068_000066.xhtml -> ../html-full/dir_000068_000066.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structLocalSettleData-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structLocalSettleData-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structLocalSettleData-members.xhtml -> ../html-full/structLocalSettleData-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_39.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_48.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_39.png -> ../html-full/form_48.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000068.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000068.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000068.xhtml -> ../html-full/dir_000017_000068.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmap__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmap__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmap__t-members.xhtml -> ../html-full/structgmx__cmap__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structNumPmeDomains-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structNumPmeDomains-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structNumPmeDomains-members.xhtml -> ../html-full/structNumPmeDomains-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structIndexGroup-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structIndexGroup-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structIndexGroup-members.xhtml -> ../html-full/structIndexGroup-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000014.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000014.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000014.xhtml -> ../html-full/dir_000017_000014.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000007.xhtml -> ../html-full/dir_000017_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000014.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000014.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000014.xhtml -> ../html-full/dir_000025_000014.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000073.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000073.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000073.xhtml -> ../html-full/dir_000021_000073.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysisdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysisdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/analysisdata_8h__incl.svg -> ../html-full/analysisdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000061.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000061.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000061.xhtml -> ../html-full/dir_000025_000061.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000068.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000068.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000068.xhtml -> ../html-full/dir_000021_000068.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__xpmelmt-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__xpmelmt-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__xpmelmt-members.xhtml -> ../html-full/structt__xpmelmt-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000083.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000083.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000083.xhtml -> ../html-full/dir_000025_000083.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000052.xhtml -> ../html-full/dir_000017_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000014_000061.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000014_000061.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000014_000061.xhtml -> ../html-full/dir_000014_000061.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000077.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000077.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000077.xhtml -> ../html-full/dir_000025_000077.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPpRanks-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPpRanks-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPpRanks-members.xhtml -> ../html-full/structPpRanks-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1OutputSelectorDeathTest__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1OutputSelectorDeathTest__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1OutputSelectorDeathTest__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000018.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000071_000018.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000071_000018.xhtml -> ../html-full/dir_000071_000018.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000007.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000024_000007.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000024_000007.xhtml -> ../html-full/dir_000024_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000061.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000061.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000061.xhtml -> ../html-full/dir_000160_000061.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000065.xhtml -> ../html-full/dir_000090_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000065.xhtml -> ../html-full/dir_000160_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000103_000052.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000103_000052.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000103_000052.xhtml -> ../html-full/dir_000103_000052.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000040.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000025_000040.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000025_000040.xhtml -> ../html-full/dir_000025_000040.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000106_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000106_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000106_000069.xhtml -> ../html-full/dir_000106_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000069.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000023_000069.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000069.xhtml -> ../html-full/dir_000023_000069.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000014_000066.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000014_000066.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000014_000066.xhtml -> ../html-full/dir_000014_000066.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1AnyOutputSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> ../html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000065.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000072_000065.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000072_000065.xhtml -> ../html-full/dir_000072_000065.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000040.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000040.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000040.xhtml -> ../html-full/dir_000065_000040.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError__inherit__graph.svg -> ../html-full/classgmx_1_1APIError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioutputadapter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ioutputadapter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ioutputadapter_8h__incl.svg -> ../html-full/ioutputadapter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func_y.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/functions_func_y.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func_y.xhtml -> ../html-full/functions_func_y.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_0.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_0.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_0.png -> ../html-full/form_0.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AlignedArray_3_01double_00_01N_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AlignedArray_3_01double_00_01N_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AlignedArray_3_01double_00_01N_01_4-members.xhtml -> ../html-full/structgmx_1_1AlignedArray_3_01double_00_01N_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ewald__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ewald__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ewald__utils_8h__incl.svg -> ../html-full/ewald__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AlignedArray_3_01float_00_01N_01_4-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1AlignedArray_3_01float_00_01N_01_4-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1AlignedArray_3_01float_00_01N_01_4-members.xhtml -> ../html-full/structgmx_1_1AlignedArray_3_01float_00_01N_01_4-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer_8h__incl.svg -> ../html-full/gpuregiontimer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_0_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_0_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_0_dark.png -> ../html-full/form_0_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__random.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__random.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__random.svg -> ../html-full/group__module__random.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ifunc_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8cpp__incl.svg -> ../html-full/ifunc_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_j.xhtml -> ../html-full/namespacemembers_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmapdata__t-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__cmapdata__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__cmapdata__t-members.xhtml -> ../html-full/structgmx__cmapdata__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/message__string__collector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/message__string__collector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/message__string__collector_8h__incl.svg -> ../html-full/message__string__collector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_k.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_k.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_k.xhtml -> ../html-full/namespacemembers_func_k.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError__inherit__graph.svg -> ../html-full/classgmx_1_1UserInputError__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_x.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_x.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_x.xhtml -> ../html-full/namespacemembers_func_x.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_func_v.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/globals_func_v.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_func_v.xhtml -> ../html-full/globals_func_v.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/timeunitmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/timeunitmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/timeunitmanager_8h__incl.svg -> ../html-full/timeunitmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__restraint.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__restraint.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__restraint.svg -> ../html-full/group__module__restraint.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_1.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_1.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_1.png -> ../html-full/form_1.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__listed__forces.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__listed__forces.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__listed__forces.svg -> ../html-full/group__module__listed__forces.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_1_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_1_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_1_dark.png -> ../html-full/form_1_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputStream__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputStream__inherit__graph.svg -> ../html-full/classgmx_1_1TextInputStream__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sysinfo_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sysinfo_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sysinfo_8h__incl.svg -> ../html-full/sysinfo_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pages.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pages.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pages.xhtml -> ../html-full/pages.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesAtomsRedistributedSignal__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesAtomsRedistributedSignal__coll__graph.svg -> ../html-full/structgmx_1_1MDModulesAtomsRedistributedSignal__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionbehavior_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionbehavior_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionoptionbehavior_8h__incl.svg -> ../html-full/selectionoptionbehavior_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_func_h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/globals_func_h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/globals_func_h.xhtml -> ../html-full/globals_func_h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_j.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func_j.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func_j.xhtml -> ../html-full/namespacemembers_func_j.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers_func.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers_func.xhtml -> ../html-full/namespacemembers_func.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/namespacemembers.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/namespacemembers.xhtml -> ../html-full/namespacemembers.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSimulationGroups__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSimulationGroups__coll__graph.svg -> ../html-full/structSimulationGroups__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__enerdata__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__enerdata__t__coll__graph.svg -> ../html-full/structgmx__enerdata__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/behaviorcollection_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/behaviorcollection_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/behaviorcollection_8h__incl.svg -> ../html-full/behaviorcollection_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/partition_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/partition_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/partition_8h__incl.svg -> ../html-full/partition_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__stream_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__stream_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__stream_8h__incl.svg -> ../html-full/device__stream_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/functions_func.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions_func.xhtml -> ../html-full/functions_func.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderopen.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderopen.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderopen.svg -> ../html-full/folderopen.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/functions__.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/functions.xhtml -> ../html-full/functions__.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textblockmatchers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textblockmatchers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textblockmatchers_8h__incl.svg -> ../html-full/textblockmatchers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_27.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_29.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_27.png -> ../html-full/form_29.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/statistics_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/statistics_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/statistics_8h__incl.svg -> ../html-full/statistics_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg -> ../html-full/structgmx_1_1NbnxmPairlistCpuWork__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/basedefinitions_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/basedefinitions_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/basedefinitions_8h__incl.svg -> ../html-full/basedefinitions_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testfilemanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testfilemanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testfilemanager_8h__incl.svg -> ../html-full/testfilemanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderopend.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderopend.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderopend.svg -> ../html-full/folderopend.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__shared__amd_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__management__shared__amd_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__shared__amd_8h__incl.svg -> ../html-full/device__management__shared__amd_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__nbnxm.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__nbnxm.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__nbnxm.svg -> ../html-full/group__module__nbnxm.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/modularsimulator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/modularsimulator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/modularsimulator_8h__incl.svg -> ../html-full/modularsimulator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/printtime_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/printtime_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/printtime_8h__incl.svg -> ../html-full/printtime_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ewald_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ewald_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ewald_8h__incl.svg -> ../html-full/ewald_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_34dd9222320d41e3c3d43a608989ea3b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_34dd9222320d41e3c3d43a608989ea3b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_34dd9222320d41e3c3d43a608989ea3b_dep.svg -> ../html-full/dir_34dd9222320d41e3c3d43a608989ea3b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datamodulemanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/datamodulemanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/datamodulemanager_8h__incl.svg -> ../html-full/datamodulemanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceProviderInput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceProviderInput__coll__graph.svg -> ../html-full/classgmx_1_1ForceProviderInput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_af3696197bf82a93bf282a2e5bb38332_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_af3696197bf82a93bf282a2e5bb38332_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_af3696197bf82a93bf282a2e5bb38332_dep.svg -> ../html-full/dir_af3696197bf82a93bf282a2e5bb38332_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/examples.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/examples.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/examples.xhtml -> ../html-full/examples.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineparser_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlineparser_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineparser_8h__incl.svg -> ../html-full/cmdlineparser_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg -> ../html-full/dir_a404b2cbf9db2e547ba9696baa2a562b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d01c07398b4254f96a7150c96b79b270_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_d01c07398b4254f96a7150c96b79b270_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_d01c07398b4254f96a7150c96b79b270_dep.svg -> ../html-full/dir_d01c07398b4254f96a7150c96b79b270_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinemodulemanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinemodulemanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinemodulemanager_8h__incl.svg -> ../html-full/cmdlinemodulemanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7e013631519469366ffd6bf609372539_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_7e013631519469366ffd6bf609372539_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_7e013631519469366ffd6bf609372539_dep.svg -> ../html-full/dir_7e013631519469366ffd6bf609372539_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__taskassignment.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__taskassignment.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__taskassignment.svg -> ../html-full/group__module__taskassignment.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_27_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_29_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_27_dark.png -> ../html-full/form_29_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg -> ../html-full/dir_1cf35e38591e8e73a4382cc8c8a3cf37_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_14.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_14.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/msc_inline_mscgraph_14.svg -> ../html-full/msc_inline_mscgraph_14.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/shake_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/shake_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/shake_8h__incl.svg -> ../html-full/shake_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__idef__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__idef__coll__graph.svg -> ../html-full/structt__idef__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_3.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dot_inline_dotgraph_3.svg -> ../html-full/dot_inline_dotgraph_3.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64General__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64General__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculePatchDatabase__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculePatchDatabase__coll__graph.svg -> ../html-full/structMoleculePatchDatabase__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPreprocessResidue__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue__coll__graph.svg -> ../html-full/structPreprocessResidue__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__correlationfunctions.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__correlationfunctions.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__correlationfunctions.svg -> ../html-full/group__module__correlationfunctions.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PairsearchWork__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1PairsearchWork__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1PairsearchWork__coll__graph.svg -> ../html-full/structgmx_1_1PairsearchWork__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption__coll__graph.svg -> ../html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> ../html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg -> ../html-full/structgmx_1_1NbnxnPairlistCpu__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption__coll__graph.svg -> ../html-full/classgmx_1_1EnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOption__inherit__graph.svg -> ../html-full/classgmx_1_1EnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ModuleSelection__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ModuleSelection__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1ModuleSelection__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg -> ../html-full/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplateSimple__inherit__graph.svg -> ../html-full/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic__inherit__graph.svg -> ../html-full/classgmx_1_1CompositeHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CompositeHelpTopic__coll__graph.svg -> ../html-full/classgmx_1_1CompositeHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__imd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__imd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__imd.svg -> ../html-full/group__module__imd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__tables.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__tables.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__tables.svg -> ../html-full/group__module__tables.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__swap.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__swap.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__swap.svg -> ../html-full/group__module__swap.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetPrecisionSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocitySupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetVelocitySupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetVelocityUnSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetAtomsUnSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetAtomsSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetAtomsSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetForceSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1SetForceUnSupportedFiles__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1SetForceUnSupportedFiles__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic__inherit__graph.svg -> ../html-full/classgmx_1_1SimpleHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimpleHelpTopic__coll__graph.svg -> ../html-full/classgmx_1_1SimpleHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_12_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_12_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_12_dark.png -> ../html-full/form_12_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c428f345b527d2071b666c6f8374398_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c428f345b527d2071b666c6f8374398_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c428f345b527d2071b666c6f8374398_dep.svg -> ../html-full/dir_8c428f345b527d2071b666c6f8374398_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/defaultinitializationallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/defaultinitializationallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/defaultinitializationallocator_8h__incl.svg -> ../html-full/defaultinitializationallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> ../html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MissingElementConnectionError__coll__graph.svg -> ../html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> ../html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ParallelConsistencyError__coll__graph.svg -> ../html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iframeconverter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/iframeconverter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/iframeconverter_8h__incl.svg -> ../html-full/iframeconverter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1871851d9cfb65be92ceb250f0610eb5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_1871851d9cfb65be92ceb250f0610eb5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_1871851d9cfb65be92ceb250f0610eb5_dep.svg -> ../html-full/dir_1871851d9cfb65be92ceb250f0610eb5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull__rotation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pull__rotation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pull__rotation_8h__incl.svg -> ../html-full/pull__rotation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__sycl__intel__device__ids_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__management__sycl__intel__device__ids_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__sycl__intel__device__ids_8h__incl.svg -> ../html-full/device__management__sycl__intel__device__ids_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_12.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_12.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_12.png -> ../html-full/form_12.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6db5db4c493eb96fab49e5d6350ca481_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6db5db4c493eb96fab49e5d6350ca481_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6db5db4c493eb96fab49e5d6350ca481_dep.svg -> ../html-full/dir_6db5db4c493eb96fab49e5d6350ca481_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/clfftinitializer_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/clfftinitializer_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/clfftinitializer_8h__incl.svg -> ../html-full/clfftinitializer_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c18565c80c0a9a14eccbb55755bf1c7f_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c18565c80c0a9a14eccbb55755bf1c7f_dep.svg -> ../html-full/dir_c18565c80c0a9a14eccbb55755bf1c7f_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_df09b5ba214e360ecb99468cfd14e9e7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_df09b5ba214e360ecb99468cfd14e9e7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_df09b5ba214e360ecb99468cfd14e9e7_dep.svg -> ../html-full/dir_df09b5ba214e360ecb99468cfd14e9e7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_532bf28f355a758c5974bf4170215a92_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_532bf28f355a758c5974bf4170215a92_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_532bf28f355a758c5974bf4170215a92_dep.svg -> ../html-full/dir_532bf28f355a758c5974bf4170215a92_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1NoOptionalOutput__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption__coll__graph.svg -> ../html-full/classgmx_1_1FloatOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOption__inherit__graph.svg -> ../html-full/classgmx_1_1FloatOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOption__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option__inherit__graph.svg -> ../html-full/classgmx_1_1Int64Option__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64Option__coll__graph.svg -> ../html-full/classgmx_1_1Int64Option__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selhelp_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selhelp_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selhelp_8h__incl.svg -> ../html-full/selhelp_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_26f117cf35af0cc558c2ac47db8ebfc7_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_26f117cf35af0cc558c2ac47db8ebfc7_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_26f117cf35af0cc558c2ac47db8ebfc7_dep.svg -> ../html-full/dir_26f117cf35af0cc558c2ac47db8ebfc7_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c28e49faf0c5b3de14df07f63657b701_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_c28e49faf0c5b3de14df07f63657b701_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_c28e49faf0c5b3de14df07f63657b701_dep.svg -> ../html-full/dir_c28e49faf0c5b3de14df07f63657b701_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_55e6b9bceb5e3e08725efcf4929777ec_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_55e6b9bceb5e3e08725efcf4929777ec_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_55e6b9bceb5e3e08725efcf4929777ec_dep.svg -> ../html-full/dir_55e6b9bceb5e3e08725efcf4929777ec_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAverageHistogram__coll__graph.svg -> ../html-full/classgmx_1_1AbstractAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionManager__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionManager__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__coll__graph.svg -> ../html-full/classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__inherit__graph.svg -> ../html-full/classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/snprintf_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/snprintf_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/snprintf_8h__incl.svg -> ../html-full/snprintf_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption__inherit__graph.svg -> ../html-full/classgmx_1_1DoubleOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOption__coll__graph.svg -> ../html-full/classgmx_1_1DoubleOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6dbdbb1d21ecddcc048cc00cefbd3a78_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_6dbdbb1d21ecddcc048cc00cefbd3a78_dep.svg -> ../html-full/dir_6dbdbb1d21ecddcc048cc00cefbd3a78_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption__coll__graph.svg -> ../html-full/classgmx_1_1StringOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOption__inherit__graph.svg -> ../html-full/classgmx_1_1StringOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4d2c8473c6e5680e4aca5a3e3e5886dd_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_4d2c8473c6e5680e4aca5a3e3e5886dd_dep.svg -> ../html-full/dir_4d2c8473c6e5680e4aca5a3e3e5886dd_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOption__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pairlist__tuning_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pairlist__tuning_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pairlist__tuning_8h__incl.svg -> ../html-full/pairlist__tuning_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcherSettings__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1IFileMatcherSettings__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1IFileMatcherSettings__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1IFileMatcherSettings__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractOptionSection__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractOptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1AbstractOptionSection__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2a7e973503d881e60df68eed40a2f16a_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_2a7e973503d881e60df68eed40a2f16a_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_2a7e973503d881e60df68eed40a2f16a_dep.svg -> ../html-full/dir_2a7e973503d881e60df68eed40a2f16a_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_95717a81c2d2f4488fb73b9bd8027da2_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_95717a81c2d2f4488fb73b9bd8027da2_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_95717a81c2d2f4488fb73b9bd8027da2_dep.svg -> ../html-full/dir_95717a81c2d2f4488fb73b9bd8027da2_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options__coll__graph.svg -> ../html-full/classgmx_1_1Options__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Options__inherit__graph.svg -> ../html-full/classgmx_1_1Options__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputStream__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputStream__inherit__graph.svg -> ../html-full/classgmx_1_1TextOutputStream__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption__inherit__graph.svg -> ../html-full/classgmx_1_1BooleanOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOption__coll__graph.svg -> ../html-full/classgmx_1_1BooleanOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c6de95273a4a1ab66e54094731e47f5_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_8c6de95273a4a1ab66e54094731e47f5_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_8c6de95273a4a1ab66e54094731e47f5_dep.svg -> ../html-full/dir_8c6de95273a4a1ab66e54094731e47f5_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1IOptionsBehavior__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__energyanalysis.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__energyanalysis.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__energyanalysis.svg -> ../html-full/group__module__energyanalysis.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stdiohelper_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/stdiohelper_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/stdiohelper_8h__incl.svg -> ../html-full/stdiohelper_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/oclraii_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/oclraii_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/oclraii_8h__incl.svg -> ../html-full/oclraii_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/integrate_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/integrate_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/integrate_8h__incl.svg -> ../html-full/integrate_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractPlotModule__coll__graph.svg -> ../html-full/classgmx_1_1AbstractPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionenums_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionenums_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selectionenums_8h__incl.svg -> ../html-full/selectionenums_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bench__setup_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bench__setup_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bench__setup_8h__incl.svg -> ../html-full/bench__setup_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2domdec_2options_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/src_2gromacs_2domdec_2options_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2domdec_2options_8h__incl.svg -> ../html-full/src_2gromacs_2domdec_2options_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> ../html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ElementNotFoundError__coll__graph.svg -> ../html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError__coll__graph.svg -> ../html-full/classgmx_1_1InconsistentInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InconsistentInputError__inherit__graph.svg -> ../html-full/classgmx_1_1InconsistentInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError__coll__graph.svg -> ../html-full/classgmx_1_1CheckpointError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CheckpointError__inherit__graph.svg -> ../html-full/classgmx_1_1CheckpointError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError__coll__graph.svg -> ../html-full/classgmx_1_1InvalidInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InvalidInputError__inherit__graph.svg -> ../html-full/classgmx_1_1InvalidInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__ocl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gputraits__ocl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__ocl_8h__incl.svg -> ../html-full/gputraits__ocl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionflags_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionflags_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionflags_8h__incl.svg -> ../html-full/optionflags_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationdatabase_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationdatabase_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationdatabase_8h__incl.svg -> ../html-full/simulationdatabase_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError__inherit__graph.svg -> ../html-full/classgmx_1_1NotImplementedError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1NotImplementedError__coll__graph.svg -> ../html-full/classgmx_1_1NotImplementedError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/edsam_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/edsam_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/edsam_8h__incl.svg -> ../html-full/edsam_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setenv_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/setenv_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setenv_8h__incl.svg -> ../html-full/setenv_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359d2bec989c9a8deeeb9aee335c1c76_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_359d2bec989c9a8deeeb9aee335c1c76_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_359d2bec989c9a8deeeb9aee335c1c76_dep.svg -> ../html-full/dir_359d2bec989c9a8deeeb9aee335c1c76_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__sycl__kernel__utils_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hip__sycl__kernel__utils_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/hip__sycl__kernel__utils_8h__incl.svg -> ../html-full/hip__sycl__kernel__utils_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atominfo_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/atominfo_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/atominfo_8h__incl.svg -> ../html-full/atominfo_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/smalloc_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/smalloc_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/smalloc_8h__incl.svg -> ../html-full/smalloc_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filematchers_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/filematchers_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/filematchers_8h__incl.svg -> ../html-full/filematchers_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationsignal_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationsignal_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationsignal_8h__incl.svg -> ../html-full/simulationsignal_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__datatype_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/devicebuffer__datatype_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/devicebuffer__datatype_8h__incl.svg -> ../html-full/devicebuffer__datatype_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpwriter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinehelpwriter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinehelpwriter_8h__incl.svg -> ../html-full/cmdlinehelpwriter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpformat_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/helpformat_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpformat_8h__incl.svg -> ../html-full/helpformat_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/layouts_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/layouts_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/layouts_8h__incl.svg -> ../html-full/layouts_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsassigner_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/optionsassigner_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/optionsassigner_8h__incl.svg -> ../html-full/optionsassigner_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/extents_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/extents_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/extents_8h__incl.svg -> ../html-full/extents_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpmanager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/helpmanager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/helpmanager_8h__incl.svg -> ../html-full/helpmanager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fft_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fft_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/fft_8h__incl.svg -> ../html-full/fft_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/imd_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/imd_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/imd_8h__incl.svg -> ../html-full/imd_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MDLogger__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1MDLogger__coll__graph.svg -> ../html-full/classgmx_1_1MDLogger__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_45_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_59_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_45_dark.png -> ../html-full/form_59_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_45.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_59.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_45.png -> ../html-full/form_59.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_13_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_13_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_13_dark.png -> ../html-full/form_13_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1NumericalSplineTableInput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1NumericalSplineTableInput__coll__graph.svg -> ../html-full/structgmx_1_1NumericalSplineTableInput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mtop__atomloops_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mtop__atomloops_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mtop__atomloops_8h__incl.svg -> ../html-full/mtop__atomloops_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_13.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_13.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_13.png -> ../html-full/form_13.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Machine__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1HardwareTopology_1_1Machine__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1HardwareTopology_1_1Machine__coll__graph.svg -> ../html-full/structgmx_1_1HardwareTopology_1_1Machine__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSystemMomenta__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSystemMomenta__coll__graph.svg -> ../html-full/structSystemMomenta__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64__coll__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> ../html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GridDimensions__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GridDimensions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GridDimensions__coll__graph.svg -> ../html-full/structgmx_1_1GridDimensions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude__coll__graph.svg -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1PositionAndAmplitude__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_47_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_61_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_47_dark.png -> ../html-full/form_61_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape__coll__graph.svg -> ../html-full/structgmx_1_1GaussianSpreadKernelParameters_1_1Shape__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__awh.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__awh.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__awh.svg -> ../html-full/group__module__awh.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor__inherit__graph.svg -> ../html-full/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg -> ../html-full/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosedd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderclosedd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosedd.svg -> ../html-full/folderclosedd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosed.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderclosed.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosed.svg -> ../html-full/folderclosed.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1CoordinatesAndBoxPreprocessed__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1CoordinatesAndBoxPreprocessed__coll__graph.svg -> ../html-full/structgmx_1_1CoordinatesAndBoxPreprocessed__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/decidegpuusage_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/decidegpuusage_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/decidegpuusage_8h__incl.svg -> ../html-full/decidegpuusage_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceWithVirial__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ForceWithVirial__coll__graph.svg -> ../html-full/classgmx_1_1ForceWithVirial__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg -> ../html-full/structgmx_1_1DomainCommBackward_1_1ColumnInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__inherit__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/binaryinformation_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/binaryinformation_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/binaryinformation_8h__incl.svg -> ../html-full/binaryinformation_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg -> ../html-full/dir_785d6d0c2c6073a66ffd258f1b901773_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_46_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_60_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_46_dark.png -> ../html-full/form_60_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structDeviceInformation__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structDeviceInformation__coll__graph.svg -> ../html-full/structDeviceInformation__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__oriresdata__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__oriresdata__coll__graph.svg -> ../html-full/structt__oriresdata__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg -> ../html-full/dir_606ae0db4a6e41cf07dfbc1f9e2d7bb6_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__matrix__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__matrix__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__matrix__coll__graph.svg -> ../html-full/structt__matrix__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1MDModulesWriteCheckpointData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1MDModulesWriteCheckpointData__coll__graph.svg -> ../html-full/structgmx_1_1MDModulesWriteCheckpointData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/computemultibodycutoffs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/computemultibodycutoffs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/computemultibodycutoffs_8h__incl.svg -> ../html-full/computemultibodycutoffs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_47.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_61.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_47.png -> ../html-full/form_61.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cyclecounter_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cyclecounter_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cyclecounter_8h__incl.svg -> ../html-full/cyclecounter_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h__dep__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nrjac_8h__dep__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nrjac_8h__dep__incl.svg -> ../html-full/nrjac_8h__dep__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPartialDeserializedTprFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPartialDeserializedTprFile__coll__graph.svg -> ../html-full/structPartialDeserializedTprFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__inherit__graph.svg -> ../html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor__coll__graph.svg -> ../html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor__inherit__graph.svg -> ../html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textstream_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textstream_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textstream_8h__incl.svg -> ../html-full/textstream_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxassert_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmxassert_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxassert_8h__incl.svg -> ../html-full/gmxassert_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/read__params_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/read__params_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/read__params_8h__incl.svg -> ../html-full/read__params_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/long__range__correction_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/long__range__correction_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/long__range__correction_8h__incl.svg -> ../html-full/long__range__correction_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coolstuff_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/coolstuff_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/coolstuff_8h__incl.svg -> ../html-full/coolstuff_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typetraits_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/typetraits_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typetraits_8h__incl.svg -> ../html-full/typetraits_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractdata_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/abstractdata_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/abstractdata_8h__incl.svg -> ../html-full/abstractdata_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/crosscorr_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/crosscorr_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/crosscorr_8h__incl.svg -> ../html-full/crosscorr_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxmpi_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmxmpi_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxmpi_8h__incl.svg -> ../html-full/gmxmpi_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ifunc_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ifunc_8h__incl.svg -> ../html-full/ifunc_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate__inherit__graph.svg -> ../html-full/classgmx_1_1OptionTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionTemplate__coll__graph.svg -> ../html-full/classgmx_1_1OptionTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/polynomials_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/polynomials_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/polynomials_8h__incl.svg -> ../html-full/polynomials_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PotentialPointData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1PotentialPointData__coll__graph.svg -> ../html-full/classgmx_1_1PotentialPointData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typecasts__cuda__hip_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/typecasts__cuda__hip_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/typecasts__cuda__hip_8h__incl.svg -> ../html-full/typecasts__cuda__hip_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg -> ../html-full/classgmx_1_1IOptionsContainerWithSections__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractCompositeHelpTopic__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractCompositeHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractCompositeHelpTopic__coll__graph.svg -> ../html-full/classgmx_1_1AbstractCompositeHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> ../html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationInstabilityError__coll__graph.svg -> ../html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_46.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_60.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_46.png -> ../html-full/form_60.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg -> ../html-full/structgmx_1_1nbnxn__cj__packed__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1ConfMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1XvgMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1XvgMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1XvgMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplate__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionStorageTemplate__coll__graph.svg -> ../html-full/classgmx_1_1OptionStorageTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dlb_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dlb_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dlb_8h__incl.svg -> ../html-full/dlb_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__pos__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ana__pos__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ana__pos__t__coll__graph.svg -> ../html-full/structgmx__ana__pos__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classInteractionDefinitions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classInteractionDefinitions__coll__graph.svg -> ../html-full/classInteractionDefinitions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pleasecite_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pleasecite_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pleasecite_8h__incl.svg -> ../html-full/pleasecite_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__correlation__history_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/awh__correlation__history_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/awh__correlation__history_8h__incl.svg -> ../html-full/awh__correlation__history_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar__util_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/scalar__util_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/scalar__util_8h__incl.svg -> ../html-full/scalar__util_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1TestSystem__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1TestSystem__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1test_1_1TestSystem__coll__graph.svg -> ../html-full/structgmx_1_1test_1_1TestSystem__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__stream__manager_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__stream__manager_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__stream__manager_8h__incl.svg -> ../html-full/device__stream__manager_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localtopologychecker_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/localtopologychecker_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localtopologychecker_8h__incl.svg -> ../html-full/localtopologychecker_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection__coll__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structMoleculeInformation__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structMoleculeInformation__coll__graph.svg -> ../html-full/structMoleculeInformation__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ffparams__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ffparams__t__coll__graph.svg -> ../html-full/structgmx__ffparams__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BenchmarkSystem__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1BenchmarkSystem__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx_1_1BenchmarkSystem__coll__graph.svg -> ../html-full/structgmx_1_1BenchmarkSystem__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_22_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22_dark.png -> ../html-full/form_22_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyInput__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1LegacyInput__coll__graph.svg -> ../html-full/classgmx_1_1LegacyInput__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/programcontext_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/programcontext_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/programcontext_8h__incl.svg -> ../html-full/programcontext_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__moltype__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__moltype__t__coll__graph.svg -> ../html-full/structgmx__moltype__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__modularsimulator.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__modularsimulator.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__modularsimulator.svg -> ../html-full/group__module__modularsimulator.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/observableshistory_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/observableshistory_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/observableshistory_8h__incl.svg -> ../html-full/observableshistory_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleParallel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext__inherit__graph.svg -> ../html-full/classgmx_1_1CommandLineProgramContext__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CommandLineProgramContext__coll__graph.svg -> ../html-full/classgmx_1_1CommandLineProgramContext__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__program_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__gpu__program_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__gpu__program_8h__incl.svg -> ../html-full/pme__gpu__program_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__only_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pme__only_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pme__only_8h__incl.svg -> ../html-full/pme__only_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> ../html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ProcessFrameConversion__coll__graph.svg -> ../html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector__inherit__graph.svg -> ../html-full/classgmx_1_1OutputSelector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OutputSelector__coll__graph.svg -> ../html-full/classgmx_1_1OutputSelector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg -> ../html-full/classgmx_1_1AbstractAnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mapping__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__mapping__coll__graph.svg -> ../html-full/structt__mapping__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/electricfield_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/electricfield_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/electricfield_8h__incl.svg -> ../html-full/electricfield_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IFrameConverter__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IFrameConverter__inherit__graph.svg -> ../html-full/classgmx_1_1IFrameConverter__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testarrayrefs_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/testarrayrefs_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/testarrayrefs_8h__incl.svg -> ../html-full/testarrayrefs_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisDataModuleSerial__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dlbtiming_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dlbtiming_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dlbtiming_8h__incl.svg -> ../html-full/dlbtiming_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities__coll__graph.svg -> ../html-full/classgmx_1_1SetVelocities__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetVelocities__inherit__graph.svg -> ../html-full/classgmx_1_1SetVelocities__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_34_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_36_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_34_dark.png -> ../html-full/form_36_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FlagTest__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1FlagTest__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinemodule_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinemodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlinemodule_8h__incl.svg -> ../html-full/cmdlinemodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption__coll__graph.svg -> ../html-full/classgmx_1_1SelectionFileOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionFileOption__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionFileOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionManager__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrun__integration__tests.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__mdrun__integration__tests.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrun__integration__tests.svg -> ../html-full/group__module__mdrun__integration__tests.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FloatOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep__coll__graph.svg -> ../html-full/classgmx_1_1SetTimeStep__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetTimeStep__inherit__graph.svg -> ../html-full/classgmx_1_1SetTimeStep__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision__inherit__graph.svg -> ../html-full/classgmx_1_1SetPrecision__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetPrecision__coll__graph.svg -> ../html-full/classgmx_1_1SetPrecision__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__support_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simd__support_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simd__support_8h__incl.svg -> ../html-full/simd__support_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_31_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_33_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_31_dark.png -> ../html-full/form_33_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1NoContentsMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_26_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_26_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_26_dark.png -> ../html-full/form_26_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime__inherit__graph.svg -> ../html-full/classgmx_1_1SetStartTime__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetStartTime__coll__graph.svg -> ../html-full/classgmx_1_1SetStartTime__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localtopology_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/localtopology_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localtopology_8h__incl.svg -> ../html-full/localtopology_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior__coll__graph.svg -> ../html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractSimpleHelpTopic__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AbstractSimpleHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AbstractSimpleHelpTopic__coll__graph.svg -> ../html-full/classgmx_1_1AbstractSimpleHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1StringOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1StringOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces__coll__graph.svg -> ../html-full/classgmx_1_1SetForces__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetForces__inherit__graph.svg -> ../html-full/classgmx_1_1SetForces__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1DoubleOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxopencl_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gmxopencl_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gmxopencl_8h__incl.svg -> ../html-full/gmxopencl_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pullhistory_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/pullhistory_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pullhistory_8h__incl.svg -> ../html-full/pullhistory_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__inherit__graph.svg -> ../html-full/classgmx_1_1StringOutputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__coll__graph.svg -> ../html-full/classgmx_1_1StringOutputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__hip_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gputraits__hip_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits__hip_8h__incl.svg -> ../html-full/gputraits__hip_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> ../html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileNameOptionManager__coll__graph.svg -> ../html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gputraits_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gputraits_8h__incl.svg -> ../html-full/gputraits_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError__inherit__graph.svg -> ../html-full/classgmx_1_1ToleranceError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ToleranceError__coll__graph.svg -> ../html-full/classgmx_1_1ToleranceError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/imdoutputprovider_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/imdoutputprovider_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/imdoutputprovider_8h__incl.svg -> ../html-full/imdoutputprovider_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo__coll__graph.svg -> ../html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> ../html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> ../html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TimeUnitBehavior__coll__graph.svg -> ../html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/accessor__policy_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/accessor__policy_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/accessor__policy_8h__incl.svg -> ../html-full/accessor__policy_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms__coll__graph.svg -> ../html-full/classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetAtoms__inherit__graph.svg -> ../html-full/classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/flags_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/flags_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/flags_8h__incl.svg -> ../html-full/flags_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_22.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_22.png -> ../html-full/form_22.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox__inherit__graph.svg -> ../html-full/classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SetBox__coll__graph.svg -> ../html-full/classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1TestException__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TestException__coll__graph.svg -> ../html-full/classgmx_1_1test_1_1TestException__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulatorError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ModularSimulatorError__coll__graph.svg -> ../html-full/classgmx_1_1ModularSimulatorError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_26.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_26.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_26.png -> ../html-full/form_26.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection__coll__graph.svg -> ../html-full/classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionSection__inherit__graph.svg -> ../html-full/classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream__coll__graph.svg -> ../html-full/classgmx_1_1StandardInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StandardInputStream__inherit__graph.svg -> ../html-full/classgmx_1_1StandardInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ihelptopic_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/ihelptopic_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/ihelptopic_8h__incl.svg -> ../html-full/ihelptopic_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomset_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/localatomset_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/localatomset_8h__incl.svg -> ../html-full/localatomset_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError__inherit__graph.svg -> ../html-full/classgmx_1_1RangeError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RangeError__coll__graph.svg -> ../html-full/classgmx_1_1RangeError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UserInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1UserInputError__coll__graph.svg -> ../html-full/classgmx_1_1UserInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData__coll__graph.svg -> ../html-full/classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisData__inherit__graph.svg -> ../html-full/classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError__inherit__graph.svg -> ../html-full/classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1InternalError__coll__graph.svg -> ../html-full/classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm__enums_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nbnxm__enums_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nbnxm__enums_8h__incl.svg -> ../html-full/nbnxm__enums_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nblist_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nblist_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nblist_8h__incl.svg -> ../html-full/nblist_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_36_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_38_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_36_dark.png -> ../html-full/form_38_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream__inherit__graph.svg -> ../html-full/classgmx_1_1StringInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringInputStream__coll__graph.svg -> ../html-full/classgmx_1_1StringInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_31.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_33.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_31.png -> ../html-full/form_33.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1INNPotModel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1INNPotModel__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1INNPotModel__inherit__graph.svg -> ../html-full/classgmx_1_1INNPotModel__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError__coll__graph.svg -> ../html-full/classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1FileIOError__inherit__graph.svg -> ../html-full/classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel__inherit__graph.svg -> ../html-full/classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TorchModel__coll__graph.svg -> ../html-full/classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_34.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_36.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_34.png -> ../html-full/form_36.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule__coll__graph.svg -> ../html-full/classgmx_1_1RestraintMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RestraintMDModule__inherit__graph.svg -> ../html-full/classgmx_1_1RestraintMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_33_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_35_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_33_dark.png -> ../html-full/form_35_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile__coll__graph.svg -> ../html-full/classgmx_1_1TextInputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextInputFile__inherit__graph.svg -> ../html-full/classgmx_1_1TextInputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1APIError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1APIError__coll__graph.svg -> ../html-full/classgmx_1_1APIError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile__coll__graph.svg -> ../html-full/classgmx_1_1TextOutputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextOutputFile__inherit__graph.svg -> ../html-full/classgmx_1_1TextOutputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_33.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_35.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_33.png -> ../html-full/form_35.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationinputhandle_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/simulationinputhandle_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/simulationinputhandle_8h__incl.svg -> ../html-full/simulationinputhandle_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_36.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_38.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_36.png -> ../html-full/form_38.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2mimic_2utilities_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/src_2gromacs_2mimic_2utilities_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2mimic_2utilities_8h__incl.svg -> ../html-full/src_2gromacs_2mimic_2utilities_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodules_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdmodules_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodules_8h__incl.svg -> ../html-full/mdmodules_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_471.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_857.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_471.svg -> ../html-full/inherit_graph_857.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_35_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_37_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_35_dark.png -> ../html-full/form_37_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/docd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/docd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/docd.svg -> ../html-full/docd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doc.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doc.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/doc.svg -> ../html-full/doc.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_43_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_52_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_43_dark.png -> ../html-full/form_52_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg -> ../html-full/dir_0188a3e6da905bc60aceb35bf790b8c9_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_051edbf3de11cf568168f65483ae264b_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_051edbf3de11cf568168f65483ae264b_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_051edbf3de11cf568168f65483ae264b_dep.svg -> ../html-full/dir_051edbf3de11cf568168f65483ae264b_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_17cbbc99af1269e66445656231b09878_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_17cbbc99af1269e66445656231b09878_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_17cbbc99af1269e66445656231b09878_dep.svg -> ../html-full/dir_17cbbc99af1269e66445656231b09878_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_37_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_39_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_37_dark.png -> ../html-full/form_39_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg -> ../html-full/dir_0ab95ba374ced1ab8f2104a2631bbc0c_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg -> ../html-full/dir_3dfde880c4fe7255f4f58a755a0d4b27_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_43.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_52.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_43.png -> ../html-full/form_52.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_35.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_37.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_35.png -> ../html-full/form_37.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_169.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_327.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_169.svg -> ../html-full/inherit_graph_327.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg -> ../html-full/dir_b0856f6b0d80ccb263b2f415c91f9e17_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_124.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_270.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_124.svg -> ../html-full/inherit_graph_270.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_123.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_269.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_123.svg -> ../html-full/inherit_graph_269.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_125.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_271.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_125.svg -> ../html-full/inherit_graph_271.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__symbuf__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structt__symbuf__coll__graph.svg -> ../html-full/structt__symbuf__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_118.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_260.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_118.svg -> ../html-full/inherit_graph_260.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_37.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_39.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_37.png -> ../html-full/form_39.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_476.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_862.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_476.svg -> ../html-full/inherit_graph_862.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_296.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_516.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_296.svg -> ../html-full/inherit_graph_516.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_297.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_517.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_297.svg -> ../html-full/inherit_graph_517.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_299.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_519.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_299.svg -> ../html-full/inherit_graph_519.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_340.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_580.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_340.svg -> ../html-full/inherit_graph_580.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_300.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_520.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_300.svg -> ../html-full/inherit_graph_520.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_75.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_174.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_75.svg -> ../html-full/inherit_graph_174.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_168.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_326.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_168.svg -> ../html-full/inherit_graph_326.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_170.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_328.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_170.svg -> ../html-full/inherit_graph_328.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_178.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_336.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_178.svg -> ../html-full/inherit_graph_336.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_84.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_196.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_84.svg -> ../html-full/inherit_graph_196.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_161.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_319.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_161.svg -> ../html-full/inherit_graph_319.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_72.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_169.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_72.svg -> ../html-full/inherit_graph_169.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_473.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_859.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_473.svg -> ../html-full/inherit_graph_859.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_460.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_776.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_460.svg -> ../html-full/inherit_graph_776.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_472.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_858.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_472.svg -> ../html-full/inherit_graph_858.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_477.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_863.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_477.svg -> ../html-full/inherit_graph_863.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_320.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_549.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_320.svg -> ../html-full/inherit_graph_549.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_122.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_268.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_122.svg -> ../html-full/inherit_graph_268.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_119.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_261.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_119.svg -> ../html-full/inherit_graph_261.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_342.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_582.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_342.svg -> ../html-full/inherit_graph_582.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_343.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_585.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_343.svg -> ../html-full/inherit_graph_585.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_167.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_325.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_167.svg -> ../html-full/inherit_graph_325.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_475.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_861.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_475.svg -> ../html-full/inherit_graph_861.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_186.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_345.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_186.svg -> ../html-full/inherit_graph_345.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_160.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_318.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_160.svg -> ../html-full/inherit_graph_318.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_166.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_324.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_166.svg -> ../html-full/inherit_graph_324.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_181.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_339.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_181.svg -> ../html-full/inherit_graph_339.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_104.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_241.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_104.svg -> ../html-full/inherit_graph_241.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_164.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_322.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_164.svg -> ../html-full/inherit_graph_322.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_185.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_344.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_185.svg -> ../html-full/inherit_graph_344.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_175.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_333.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_175.svg -> ../html-full/inherit_graph_333.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_163.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_321.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_163.svg -> ../html-full/inherit_graph_321.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_165.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_323.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_165.svg -> ../html-full/inherit_graph_323.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_159.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_317.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_159.svg -> ../html-full/inherit_graph_317.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_173.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_331.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_173.svg -> ../html-full/inherit_graph_331.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_147.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_304.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_147.svg -> ../html-full/inherit_graph_304.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_105.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_242.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_105.svg -> ../html-full/inherit_graph_242.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_338.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_578.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_338.svg -> ../html-full/inherit_graph_578.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_182.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_340.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_182.svg -> ../html-full/inherit_graph_340.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_339.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_579.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_339.svg -> ../html-full/inherit_graph_579.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_150.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_308.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_150.svg -> ../html-full/inherit_graph_308.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_74.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_172.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_74.svg -> ../html-full/inherit_graph_172.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_162.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_320.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_162.svg -> ../html-full/inherit_graph_320.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_188.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_348.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_188.svg -> ../html-full/inherit_graph_348.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_184.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_343.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_184.svg -> ../html-full/inherit_graph_343.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_180.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_338.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_180.svg -> ../html-full/inherit_graph_338.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_146.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_303.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_146.svg -> ../html-full/inherit_graph_303.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_174.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_332.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_174.svg -> ../html-full/inherit_graph_332.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_73.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_171.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_73.svg -> ../html-full/inherit_graph_171.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_385.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_648.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_385.svg -> ../html-full/inherit_graph_648.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_547.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1025.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_547.svg -> ../html-full/inherit_graph_1025.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_479.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_867.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_479.svg -> ../html-full/inherit_graph_867.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_218.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_388.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_218.svg -> ../html-full/inherit_graph_388.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_138.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_292.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_138.svg -> ../html-full/inherit_graph_292.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_136.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_290.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_136.svg -> ../html-full/inherit_graph_290.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_462.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_779.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_462.svg -> ../html-full/inherit_graph_779.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_392.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_655.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_392.svg -> ../html-full/inherit_graph_655.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_251.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_453.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_251.svg -> ../html-full/inherit_graph_453.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_137.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_291.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_137.svg -> ../html-full/inherit_graph_291.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_317.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_546.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_317.svg -> ../html-full/inherit_graph_546.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_345.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_589.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_345.svg -> ../html-full/inherit_graph_589.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_391.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_654.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_391.svg -> ../html-full/inherit_graph_654.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_219.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_389.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_219.svg -> ../html-full/inherit_graph_389.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_236.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_431.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_236.svg -> ../html-full/inherit_graph_431.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_282.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_504.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_282.svg -> ../html-full/inherit_graph_504.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_467.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_786.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_467.svg -> ../html-full/inherit_graph_786.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_470.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_856.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_470.svg -> ../html-full/inherit_graph_856.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_117.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_259.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_117.svg -> ../html-full/inherit_graph_259.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_290.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_510.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_290.svg -> ../html-full/inherit_graph_510.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_318.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_547.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_318.svg -> ../html-full/inherit_graph_547.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_41.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_88.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_41.svg -> ../html-full/inherit_graph_88.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_316.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_545.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_316.svg -> ../html-full/inherit_graph_545.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_319.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_548.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_319.svg -> ../html-full/inherit_graph_548.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_289.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_509.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_289.svg -> ../html-full/inherit_graph_509.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_298.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_518.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_298.svg -> ../html-full/inherit_graph_518.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_315.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_544.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_315.svg -> ../html-full/inherit_graph_544.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_191.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_351.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_191.svg -> ../html-full/inherit_graph_351.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_486.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_883.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_486.svg -> ../html-full/inherit_graph_883.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_141.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_298.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_141.svg -> ../html-full/inherit_graph_298.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_359.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_613.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_359.svg -> ../html-full/inherit_graph_613.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_466.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_785.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_466.svg -> ../html-full/inherit_graph_785.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_197.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_357.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_197.svg -> ../html-full/inherit_graph_357.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_293.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_513.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_293.svg -> ../html-full/inherit_graph_513.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_44.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_105.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_44.svg -> ../html-full/inherit_graph_105.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_106.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_243.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_106.svg -> ../html-full/inherit_graph_243.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_522.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_962.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_522.svg -> ../html-full/inherit_graph_962.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_488.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_889.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_488.svg -> ../html-full/inherit_graph_889.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_487.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_887.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_487.svg -> ../html-full/inherit_graph_887.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_46.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_107.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_46.svg -> ../html-full/inherit_graph_107.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_47.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_108.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_47.svg -> ../html-full/inherit_graph_108.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_519.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_959.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_519.svg -> ../html-full/inherit_graph_959.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_511.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_945.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_511.svg -> ../html-full/inherit_graph_945.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_221.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_392.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_221.svg -> ../html-full/inherit_graph_392.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_241.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_436.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_241.svg -> ../html-full/inherit_graph_436.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_98.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_229.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_98.svg -> ../html-full/inherit_graph_229.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_478.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_866.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_478.svg -> ../html-full/inherit_graph_866.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_314.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_543.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_314.svg -> ../html-full/inherit_graph_543.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_203.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_367.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_203.svg -> ../html-full/inherit_graph_367.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_461.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_778.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_461.svg -> ../html-full/inherit_graph_778.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_285.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_507.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_285.svg -> ../html-full/inherit_graph_507.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_103.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_240.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_103.svg -> ../html-full/inherit_graph_240.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_465.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_784.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_465.svg -> ../html-full/inherit_graph_784.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_260.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_461.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_260.svg -> ../html-full/inherit_graph_461.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_140.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_294.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_140.svg -> ../html-full/inherit_graph_294.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_381.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_643.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_381.svg -> ../html-full/inherit_graph_643.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_135.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_289.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_135.svg -> ../html-full/inherit_graph_289.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_38.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_85.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_38.svg -> ../html-full/inherit_graph_85.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_128.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_278.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_128.svg -> ../html-full/inherit_graph_278.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_358.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_611.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_358.svg -> ../html-full/inherit_graph_611.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_190.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_350.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_190.svg -> ../html-full/inherit_graph_350.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_332.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_565.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_332.svg -> ../html-full/inherit_graph_565.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_237.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_432.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_237.svg -> ../html-full/inherit_graph_432.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_216.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_385.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_216.svg -> ../html-full/inherit_graph_385.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_464.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_783.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_464.svg -> ../html-full/inherit_graph_783.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_367.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_627.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_367.svg -> ../html-full/inherit_graph_627.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_199.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_359.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_199.svg -> ../html-full/inherit_graph_359.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_205.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_369.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_205.svg -> ../html-full/inherit_graph_369.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_482.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_875.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_482.svg -> ../html-full/inherit_graph_875.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_34.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_81.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_34.svg -> ../html-full/inherit_graph_81.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_240.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_435.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_240.svg -> ../html-full/inherit_graph_435.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_45.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_106.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_45.svg -> ../html-full/inherit_graph_106.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_217.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_387.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_217.svg -> ../html-full/inherit_graph_387.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_334.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_568.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_334.svg -> ../html-full/inherit_graph_568.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_333.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_566.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_333.svg -> ../html-full/inherit_graph_566.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_130.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_280.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_130.svg -> ../html-full/inherit_graph_280.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_239.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_434.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_239.svg -> ../html-full/inherit_graph_434.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_25.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_60.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_25.svg -> ../html-full/inherit_graph_60.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_403.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_682.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_403.svg -> ../html-full/inherit_graph_682.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_277.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_496.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_277.svg -> ../html-full/inherit_graph_496.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_474.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_860.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_474.svg -> ../html-full/inherit_graph_860.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_493.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_905.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_493.svg -> ../html-full/inherit_graph_905.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_234.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_429.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_234.svg -> ../html-full/inherit_graph_429.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_196.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_356.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_196.svg -> ../html-full/inherit_graph_356.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_235.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_430.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_235.svg -> ../html-full/inherit_graph_430.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_233.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_428.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_233.svg -> ../html-full/inherit_graph_428.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_518.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_958.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_518.svg -> ../html-full/inherit_graph_958.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_521.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_961.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_521.svg -> ../html-full/inherit_graph_961.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_529.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_973.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_529.svg -> ../html-full/inherit_graph_973.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_238.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_433.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_238.svg -> ../html-full/inherit_graph_433.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_29.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_65.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_29.svg -> ../html-full/inherit_graph_65.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_148.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_306.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_148.svg -> ../html-full/inherit_graph_306.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_183.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_341.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_183.svg -> ../html-full/inherit_graph_341.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_382.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_644.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_382.svg -> ../html-full/inherit_graph_644.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_357.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_610.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_357.svg -> ../html-full/inherit_graph_610.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_201.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_365.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_201.svg -> ../html-full/inherit_graph_365.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_215.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_384.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_215.svg -> ../html-full/inherit_graph_384.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_362.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_622.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_362.svg -> ../html-full/inherit_graph_622.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_187.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_347.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_187.svg -> ../html-full/inherit_graph_347.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_380.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_642.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_380.svg -> ../html-full/inherit_graph_642.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_377.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_639.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_377.svg -> ../html-full/inherit_graph_639.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_378.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_640.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_378.svg -> ../html-full/inherit_graph_640.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_376.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_638.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_376.svg -> ../html-full/inherit_graph_638.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_172.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_330.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_172.svg -> ../html-full/inherit_graph_330.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_171.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_329.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_171.svg -> ../html-full/inherit_graph_329.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_379.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_641.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_379.svg -> ../html-full/inherit_graph_641.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_179.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_337.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_179.svg -> ../html-full/inherit_graph_337.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_68.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_159.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_68.svg -> ../html-full/inherit_graph_159.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_155.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_313.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_155.svg -> ../html-full/inherit_graph_313.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_383.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_645.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_383.svg -> ../html-full/inherit_graph_645.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_157.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_315.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_157.svg -> ../html-full/inherit_graph_315.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_156.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_314.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_156.svg -> ../html-full/inherit_graph_314.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_154.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_312.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_154.svg -> ../html-full/inherit_graph_312.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_189.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_349.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_189.svg -> ../html-full/inherit_graph_349.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_153.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_311.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_153.svg -> ../html-full/inherit_graph_311.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_520.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_960.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_520.svg -> ../html-full/inherit_graph_960.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_151.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_309.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_151.svg -> ../html-full/inherit_graph_309.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_152.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_310.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_152.svg -> ../html-full/inherit_graph_310.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_505.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_935.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_505.svg -> ../html-full/inherit_graph_935.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_504.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_934.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_504.svg -> ../html-full/inherit_graph_934.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_202.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_366.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_202.svg -> ../html-full/inherit_graph_366.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_388.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_651.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_388.svg -> ../html-full/inherit_graph_651.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_69.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_160.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_69.svg -> ../html-full/inherit_graph_160.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_26.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_62.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_26.svg -> ../html-full/inherit_graph_62.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_120.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_264.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_120.svg -> ../html-full/inherit_graph_264.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_50.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_137.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_50.svg -> ../html-full/inherit_graph_137.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_528.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_972.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_528.svg -> ../html-full/inherit_graph_972.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_242.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_437.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_242.svg -> ../html-full/inherit_graph_437.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_55.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_143.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_55.svg -> ../html-full/inherit_graph_143.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_398.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_665.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_398.svg -> ../html-full/inherit_graph_665.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_57.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_147.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_57.svg -> ../html-full/inherit_graph_147.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_85.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_203.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_85.svg -> ../html-full/inherit_graph_203.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_341.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_581.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_341.svg -> ../html-full/inherit_graph_581.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_206.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_370.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_206.svg -> ../html-full/inherit_graph_370.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_131.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_283.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_131.svg -> ../html-full/inherit_graph_283.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_61.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_151.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_61.svg -> ../html-full/inherit_graph_151.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_28.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_64.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_28.svg -> ../html-full/inherit_graph_64.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_305.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_531.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_305.svg -> ../html-full/inherit_graph_531.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_63.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_153.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_63.svg -> ../html-full/inherit_graph_153.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_248.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_448.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_248.svg -> ../html-full/inherit_graph_448.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_51.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_138.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_51.svg -> ../html-full/inherit_graph_138.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_337.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_575.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_337.svg -> ../html-full/inherit_graph_575.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_60.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_150.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_60.svg -> ../html-full/inherit_graph_150.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_18.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_51.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_18.svg -> ../html-full/inherit_graph_51.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_390.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_653.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_390.svg -> ../html-full/inherit_graph_653.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_204.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_368.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_204.svg -> ../html-full/inherit_graph_368.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_389.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_652.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_389.svg -> ../html-full/inherit_graph_652.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_304.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_529.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_304.svg -> ../html-full/inherit_graph_529.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_59.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_149.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_59.svg -> ../html-full/inherit_graph_149.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_139.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_293.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_139.svg -> ../html-full/inherit_graph_293.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_53.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_140.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_53.svg -> ../html-full/inherit_graph_140.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_335.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_570.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_335.svg -> ../html-full/inherit_graph_570.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_252.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_454.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_252.svg -> ../html-full/inherit_graph_454.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_54.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_141.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_54.svg -> ../html-full/inherit_graph_141.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_52.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_139.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_52.svg -> ../html-full/inherit_graph_139.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_58.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_148.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_58.svg -> ../html-full/inherit_graph_148.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_56.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_146.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_56.svg -> ../html-full/inherit_graph_146.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_266.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_470.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_266.svg -> ../html-full/inherit_graph_470.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_213.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_379.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_213.svg -> ../html-full/inherit_graph_379.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_458.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_774.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_458.svg -> ../html-full/inherit_graph_774.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_295.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_515.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_295.svg -> ../html-full/inherit_graph_515.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_91.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_219.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_91.svg -> ../html-full/inherit_graph_219.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_441.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_755.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_441.svg -> ../html-full/inherit_graph_755.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_114.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_253.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_114.svg -> ../html-full/inherit_graph_253.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_404.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_683.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_404.svg -> ../html-full/inherit_graph_683.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_369.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_630.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_369.svg -> ../html-full/inherit_graph_630.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_546.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1024.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_546.svg -> ../html-full/inherit_graph_1024.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_292.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_512.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_292.svg -> ../html-full/inherit_graph_512.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_557.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1037.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_557.svg -> ../html-full/inherit_graph_1037.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_214.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_380.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_214.svg -> ../html-full/inherit_graph_380.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_355.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_608.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_355.svg -> ../html-full/inherit_graph_608.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_459.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_775.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_459.svg -> ../html-full/inherit_graph_775.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_43.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_104.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_43.svg -> ../html-full/inherit_graph_104.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_373.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_635.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_373.svg -> ../html-full/inherit_graph_635.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_220.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_390.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_220.svg -> ../html-full/inherit_graph_390.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_480.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_873.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_480.svg -> ../html-full/inherit_graph_873.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_132.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_284.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_132.svg -> ../html-full/inherit_graph_284.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_82.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_188.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_82.svg -> ../html-full/inherit_graph_188.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_321.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_550.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_321.svg -> ../html-full/inherit_graph_550.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_33.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_78.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_33.svg -> ../html-full/inherit_graph_78.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_36.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_83.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_36.svg -> ../html-full/inherit_graph_83.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_93.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_223.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_93.svg -> ../html-full/inherit_graph_223.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_127.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_277.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_127.svg -> ../html-full/inherit_graph_277.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_92.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_221.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_92.svg -> ../html-full/inherit_graph_221.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_142.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_299.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_142.svg -> ../html-full/inherit_graph_299.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_418.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_723.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_418.svg -> ../html-full/inherit_graph_723.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_303.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_528.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_303.svg -> ../html-full/inherit_graph_528.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_97.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_228.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_97.svg -> ../html-full/inherit_graph_228.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_384.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_647.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_384.svg -> ../html-full/inherit_graph_647.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_129.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_279.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_129.svg -> ../html-full/inherit_graph_279.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_30.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_69.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_30.svg -> ../html-full/inherit_graph_69.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_517.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_957.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_517.svg -> ../html-full/inherit_graph_957.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_310.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_538.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_310.svg -> ../html-full/inherit_graph_538.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_349.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_598.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_349.svg -> ../html-full/inherit_graph_598.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_496.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_910.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_496.svg -> ../html-full/inherit_graph_910.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_327.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_557.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_327.svg -> ../html-full/inherit_graph_557.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_225.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_409.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_225.svg -> ../html-full/inherit_graph_409.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_210.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_376.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_210.svg -> ../html-full/inherit_graph_376.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_87.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_208.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_87.svg -> ../html-full/inherit_graph_208.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_527.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_969.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_527.svg -> ../html-full/inherit_graph_969.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_108.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_245.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_108.svg -> ../html-full/inherit_graph_245.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_311.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_539.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_311.svg -> ../html-full/inherit_graph_539.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_603.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1140.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_603.svg -> ../html-full/inherit_graph_1140.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_198.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_358.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_198.svg -> ../html-full/inherit_graph_358.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_419.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_726.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_419.svg -> ../html-full/inherit_graph_726.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_453.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_769.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_453.svg -> ../html-full/inherit_graph_769.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_322.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_551.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_322.svg -> ../html-full/inherit_graph_551.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_224.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_408.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_224.svg -> ../html-full/inherit_graph_408.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_40.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_87.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_40.svg -> ../html-full/inherit_graph_87.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_400.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_670.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_400.svg -> ../html-full/inherit_graph_670.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_229.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_424.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_229.svg -> ../html-full/inherit_graph_424.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_344.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_588.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_344.svg -> ../html-full/inherit_graph_588.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_494.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_907.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_494.svg -> ../html-full/inherit_graph_907.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_133.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_286.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_133.svg -> ../html-full/inherit_graph_286.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_572.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1079.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_572.svg -> ../html-full/inherit_graph_1079.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_515.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_954.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_515.svg -> ../html-full/inherit_graph_954.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_485.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_879.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_485.svg -> ../html-full/inherit_graph_879.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_396.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_663.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_396.svg -> ../html-full/inherit_graph_663.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_66.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_157.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_66.svg -> ../html-full/inherit_graph_157.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_535.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_987.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_535.svg -> ../html-full/inherit_graph_987.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_492.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_904.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_492.svg -> ../html-full/inherit_graph_904.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_489.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_897.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_489.svg -> ../html-full/inherit_graph_897.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_516.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_956.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_516.svg -> ../html-full/inherit_graph_956.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_573.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1080.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_573.svg -> ../html-full/inherit_graph_1080.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_553.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1033.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_553.svg -> ../html-full/inherit_graph_1033.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_454.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_770.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_454.svg -> ../html-full/inherit_graph_770.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_9.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_38.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_9.svg -> ../html-full/inherit_graph_38.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_281.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_503.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_281.svg -> ../html-full/inherit_graph_503.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_514.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_951.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_514.svg -> ../html-full/inherit_graph_951.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_39.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_86.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_39.svg -> ../html-full/inherit_graph_86.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_442.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_756.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_442.svg -> ../html-full/inherit_graph_756.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_89.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_215.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_89.svg -> ../html-full/inherit_graph_215.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_31.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_75.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_31.svg -> ../html-full/inherit_graph_75.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_401.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_675.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_401.svg -> ../html-full/inherit_graph_675.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_510.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_944.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_510.svg -> ../html-full/inherit_graph_944.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_526.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_968.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_526.svg -> ../html-full/inherit_graph_968.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_544.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1005.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_544.svg -> ../html-full/inherit_graph_1005.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_232.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_427.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_232.svg -> ../html-full/inherit_graph_427.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_211.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_377.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_211.svg -> ../html-full/inherit_graph_377.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_412.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_698.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_412.svg -> ../html-full/inherit_graph_698.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_399.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_668.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_399.svg -> ../html-full/inherit_graph_668.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_102.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_234.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_102.svg -> ../html-full/inherit_graph_234.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_27.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_63.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_27.svg -> ../html-full/inherit_graph_63.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_116.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_258.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_116.svg -> ../html-full/inherit_graph_258.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_560.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1046.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_560.svg -> ../html-full/inherit_graph_1046.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_192.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_352.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_192.svg -> ../html-full/inherit_graph_352.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_331.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_564.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_331.svg -> ../html-full/inherit_graph_564.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_417.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_722.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_417.svg -> ../html-full/inherit_graph_722.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_200.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_362.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_200.svg -> ../html-full/inherit_graph_362.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_360.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_616.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_360.svg -> ../html-full/inherit_graph_616.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_566.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1057.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_566.svg -> ../html-full/inherit_graph_1057.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_194.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_353.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_194.svg -> ../html-full/inherit_graph_353.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_491.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_901.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_491.svg -> ../html-full/inherit_graph_901.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_115.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_256.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_115.svg -> ../html-full/inherit_graph_256.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_468.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_854.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_468.svg -> ../html-full/inherit_graph_854.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_231.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_426.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_231.svg -> ../html-full/inherit_graph_426.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_112.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_250.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_112.svg -> ../html-full/inherit_graph_250.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_536.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_989.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_536.svg -> ../html-full/inherit_graph_989.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_444.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_758.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_444.svg -> ../html-full/inherit_graph_758.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_413.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_701.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_413.svg -> ../html-full/inherit_graph_701.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_143.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_300.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_143.svg -> ../html-full/inherit_graph_300.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_408.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_692.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_408.svg -> ../html-full/inherit_graph_692.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_395.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_662.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_395.svg -> ../html-full/inherit_graph_662.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_94.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_224.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_94.svg -> ../html-full/inherit_graph_224.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_394.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_661.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_394.svg -> ../html-full/inherit_graph_661.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_455.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_771.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_455.svg -> ../html-full/inherit_graph_771.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_397.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_664.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_397.svg -> ../html-full/inherit_graph_664.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_575.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1085.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_575.svg -> ../html-full/inherit_graph_1085.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_438.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_752.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_438.svg -> ../html-full/inherit_graph_752.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_279.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_500.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_279.svg -> ../html-full/inherit_graph_500.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_253.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_455.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_253.svg -> ../html-full/inherit_graph_455.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_565.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1052.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_565.svg -> ../html-full/inherit_graph_1052.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_452.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_768.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_452.svg -> ../html-full/inherit_graph_768.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_8.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_35.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_8.svg -> ../html-full/inherit_graph_35.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_451.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_767.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_451.svg -> ../html-full/inherit_graph_767.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_7.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_33.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_7.svg -> ../html-full/inherit_graph_33.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_20.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_53.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_20.svg -> ../html-full/inherit_graph_53.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_450.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_766.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_450.svg -> ../html-full/inherit_graph_766.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_555.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1035.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_555.svg -> ../html-full/inherit_graph_1035.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_409.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_693.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_409.svg -> ../html-full/inherit_graph_693.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_328.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_558.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_328.svg -> ../html-full/inherit_graph_558.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_372.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_634.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_372.svg -> ../html-full/inherit_graph_634.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_4.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_25.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_4.svg -> ../html-full/inherit_graph_25.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_283.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_505.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_283.svg -> ../html-full/inherit_graph_505.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_371.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_633.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_371.svg -> ../html-full/inherit_graph_633.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_212.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_378.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_212.svg -> ../html-full/inherit_graph_378.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_386.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_649.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_386.svg -> ../html-full/inherit_graph_649.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_81.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_187.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_81.svg -> ../html-full/inherit_graph_187.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_228.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_423.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_228.svg -> ../html-full/inherit_graph_423.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_508.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_940.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_508.svg -> ../html-full/inherit_graph_940.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_523.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_963.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_523.svg -> ../html-full/inherit_graph_963.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_291.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_511.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_291.svg -> ../html-full/inherit_graph_511.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_209.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_375.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_209.svg -> ../html-full/inherit_graph_375.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_37.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_84.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_37.svg -> ../html-full/inherit_graph_84.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_42.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_103.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_42.svg -> ../html-full/inherit_graph_103.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_226.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_410.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_226.svg -> ../html-full/inherit_graph_410.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_537.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_992.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_537.svg -> ../html-full/inherit_graph_992.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_457.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_773.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_457.svg -> ../html-full/inherit_graph_773.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_88.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_209.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_88.svg -> ../html-full/inherit_graph_209.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_583.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1098.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_583.svg -> ../html-full/inherit_graph_1098.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_427.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_741.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_427.svg -> ../html-full/inherit_graph_741.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_435.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_749.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_435.svg -> ../html-full/inherit_graph_749.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_361.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_618.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_361.svg -> ../html-full/inherit_graph_618.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_428.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_742.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_428.svg -> ../html-full/inherit_graph_742.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_109.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_247.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_109.svg -> ../html-full/inherit_graph_247.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_445.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_759.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_445.svg -> ../html-full/inherit_graph_759.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_145.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_302.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_145.svg -> ../html-full/inherit_graph_302.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_134.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_288.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_134.svg -> ../html-full/inherit_graph_288.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_410.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_694.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_410.svg -> ../html-full/inherit_graph_694.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_499.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_919.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_499.svg -> ../html-full/inherit_graph_919.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_17.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_50.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_17.svg -> ../html-full/inherit_graph_50.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_556.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1036.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_556.svg -> ../html-full/inherit_graph_1036.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_35.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_82.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_35.svg -> ../html-full/inherit_graph_82.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_431.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_745.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_431.svg -> ../html-full/inherit_graph_745.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_407.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_691.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_407.svg -> ../html-full/inherit_graph_691.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_434.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_748.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_434.svg -> ../html-full/inherit_graph_748.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_230.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_425.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_230.svg -> ../html-full/inherit_graph_425.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_429.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_743.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_429.svg -> ../html-full/inherit_graph_743.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_422.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_736.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_422.svg -> ../html-full/inherit_graph_736.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_558.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1040.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_558.svg -> ../html-full/inherit_graph_1040.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_433.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_747.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_433.svg -> ../html-full/inherit_graph_747.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_437.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_751.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_437.svg -> ../html-full/inherit_graph_751.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_447.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_761.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_447.svg -> ../html-full/inherit_graph_761.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_90.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_217.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_90.svg -> ../html-full/inherit_graph_217.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_370.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_631.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_370.svg -> ../html-full/inherit_graph_631.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_32.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_76.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_32.svg -> ../html-full/inherit_graph_76.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_495.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_908.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_495.svg -> ../html-full/inherit_graph_908.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_531.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_976.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_531.svg -> ../html-full/inherit_graph_976.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_80.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_180.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_80.svg -> ../html-full/inherit_graph_180.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_306.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_533.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_306.svg -> ../html-full/inherit_graph_533.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_356.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_609.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_356.svg -> ../html-full/inherit_graph_609.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_354.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_607.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_354.svg -> ../html-full/inherit_graph_607.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_405.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_689.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_405.svg -> ../html-full/inherit_graph_689.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_561.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1047.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_561.svg -> ../html-full/inherit_graph_1047.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_540.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1001.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_540.svg -> ../html-full/inherit_graph_1001.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_430.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_744.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_430.svg -> ../html-full/inherit_graph_744.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_350.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_599.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_350.svg -> ../html-full/inherit_graph_599.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_502.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_923.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_502.svg -> ../html-full/inherit_graph_923.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_424.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_738.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_424.svg -> ../html-full/inherit_graph_738.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_267.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_472.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_267.svg -> ../html-full/inherit_graph_472.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_269.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_483.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_269.svg -> ../html-full/inherit_graph_483.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_247.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_444.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_247.svg -> ../html-full/inherit_graph_444.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_443.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_757.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_443.svg -> ../html-full/inherit_graph_757.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_439.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_753.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_439.svg -> ../html-full/inherit_graph_753.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_48.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_136.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_48.svg -> ../html-full/inherit_graph_136.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_302.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_527.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_302.svg -> ../html-full/inherit_graph_527.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_144.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_301.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_144.svg -> ../html-full/inherit_graph_301.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_594.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1123.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_594.svg -> ../html-full/inherit_graph_1123.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_284.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_506.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_284.svg -> ../html-full/inherit_graph_506.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_83.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_192.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_83.svg -> ../html-full/inherit_graph_192.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_448.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_762.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_448.svg -> ../html-full/inherit_graph_762.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_275.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_493.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_275.svg -> ../html-full/inherit_graph_493.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_222.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_394.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_222.svg -> ../html-full/inherit_graph_394.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_71.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_166.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_71.svg -> ../html-full/inherit_graph_166.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_414.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_702.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_414.svg -> ../html-full/inherit_graph_702.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_336.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_571.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_336.svg -> ../html-full/inherit_graph_571.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_436.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_750.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_436.svg -> ../html-full/inherit_graph_750.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_463.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_781.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_463.svg -> ../html-full/inherit_graph_781.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_593.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1115.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_593.svg -> ../html-full/inherit_graph_1115.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_352.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_601.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_352.svg -> ../html-full/inherit_graph_601.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_563.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1049.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_563.svg -> ../html-full/inherit_graph_1049.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_308.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_535.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_308.svg -> ../html-full/inherit_graph_535.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_121.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_266.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_121.svg -> ../html-full/inherit_graph_266.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_346.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_595.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_346.svg -> ../html-full/inherit_graph_595.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_86.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_204.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_86.svg -> ../html-full/inherit_graph_204.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_324.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_553.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_324.svg -> ../html-full/inherit_graph_553.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_347.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_596.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_347.svg -> ../html-full/inherit_graph_596.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_542.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1003.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_542.svg -> ../html-full/inherit_graph_1003.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_330.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_563.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_330.svg -> ../html-full/inherit_graph_563.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_195.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_354.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_195.svg -> ../html-full/inherit_graph_354.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_509.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_942.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_509.svg -> ../html-full/inherit_graph_942.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_313.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_542.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_313.svg -> ../html-full/inherit_graph_542.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_576.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1088.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_576.svg -> ../html-full/inherit_graph_1088.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_100.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_232.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_100.svg -> ../html-full/inherit_graph_232.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_541.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1002.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_541.svg -> ../html-full/inherit_graph_1002.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_348.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_597.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_348.svg -> ../html-full/inherit_graph_597.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_548.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1027.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_548.svg -> ../html-full/inherit_graph_1027.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_268.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_482.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_268.svg -> ../html-full/inherit_graph_482.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_107.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_244.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_107.svg -> ../html-full/inherit_graph_244.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_111.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_249.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_111.svg -> ../html-full/inherit_graph_249.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_498.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_918.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_498.svg -> ../html-full/inherit_graph_918.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_113.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_251.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_113.svg -> ../html-full/inherit_graph_251.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_569.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1069.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_569.svg -> ../html-full/inherit_graph_1069.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_126.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_276.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_126.svg -> ../html-full/inherit_graph_276.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_532.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_977.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_532.svg -> ../html-full/inherit_graph_977.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_552.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1032.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_552.svg -> ../html-full/inherit_graph_1032.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_32.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_6.svg -> ../html-full/inherit_graph_32.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_11.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_41.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_11.svg -> ../html-full/inherit_graph_41.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_568.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1060.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_568.svg -> ../html-full/inherit_graph_1060.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_79.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_179.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_79.svg -> ../html-full/inherit_graph_179.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_543.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1004.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_543.svg -> ../html-full/inherit_graph_1004.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_525.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_967.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_525.svg -> ../html-full/inherit_graph_967.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_574.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1081.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_574.svg -> ../html-full/inherit_graph_1081.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_564.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1051.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_564.svg -> ../html-full/inherit_graph_1051.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_571.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1077.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_571.svg -> ../html-full/inherit_graph_1077.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_110.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_248.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_110.svg -> ../html-full/inherit_graph_248.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_416.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_707.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_416.svg -> ../html-full/inherit_graph_707.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_326.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_556.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_326.svg -> ../html-full/inherit_graph_556.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_309.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_536.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_309.svg -> ../html-full/inherit_graph_536.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_246.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_442.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_246.svg -> ../html-full/inherit_graph_442.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_387.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_650.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_387.svg -> ../html-full/inherit_graph_650.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_19.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_52.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_19.svg -> ../html-full/inherit_graph_52.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_592.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1114.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_592.svg -> ../html-full/inherit_graph_1114.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_446.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_760.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_446.svg -> ../html-full/inherit_graph_760.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_227.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_417.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_227.svg -> ../html-full/inherit_graph_417.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_539.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_997.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_539.svg -> ../html-full/inherit_graph_997.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_584.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1099.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_584.svg -> ../html-full/inherit_graph_1099.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_223.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_404.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_223.svg -> ../html-full/inherit_graph_404.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_10.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_40.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_10.svg -> ../html-full/inherit_graph_40.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_549.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1029.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_549.svg -> ../html-full/inherit_graph_1029.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_585.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1102.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_585.svg -> ../html-full/inherit_graph_1102.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_244.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_439.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_244.svg -> ../html-full/inherit_graph_439.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_0.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_19.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_0.svg -> ../html-full/inherit_graph_19.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_208.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_374.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_208.svg -> ../html-full/inherit_graph_374.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_14.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_46.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_14.svg -> ../html-full/inherit_graph_46.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_411.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_697.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_411.svg -> ../html-full/inherit_graph_697.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_20.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_1.svg -> ../html-full/inherit_graph_20.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_207.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_373.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_207.svg -> ../html-full/inherit_graph_373.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_323.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_552.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_323.svg -> ../html-full/inherit_graph_552.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_294.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_514.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_294.svg -> ../html-full/inherit_graph_514.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_351.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_600.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_351.svg -> ../html-full/inherit_graph_600.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_101.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_233.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_101.svg -> ../html-full/inherit_graph_233.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_586.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1103.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_586.svg -> ../html-full/inherit_graph_1103.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_590.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1112.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_590.svg -> ../html-full/inherit_graph_1112.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_599.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1130.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_599.svg -> ../html-full/inherit_graph_1130.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_5.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_27.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_5.svg -> ../html-full/inherit_graph_27.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_420.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_727.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_420.svg -> ../html-full/inherit_graph_727.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_261.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_462.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_261.svg -> ../html-full/inherit_graph_462.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_325.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_554.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_325.svg -> ../html-full/inherit_graph_554.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_577.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1089.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_577.svg -> ../html-full/inherit_graph_1089.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_578.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1090.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_578.svg -> ../html-full/inherit_graph_1090.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_421.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_729.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_421.svg -> ../html-full/inherit_graph_729.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_503.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_926.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_503.svg -> ../html-full/inherit_graph_926.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_588.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1110.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_588.svg -> ../html-full/inherit_graph_1110.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_415.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_706.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_415.svg -> ../html-full/inherit_graph_706.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_604.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1152.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_604.svg -> ../html-full/inherit_graph_1152.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_456.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_772.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_456.svg -> ../html-full/inherit_graph_772.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_20_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20_dark.png -> ../html-full/form_20_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_551.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1031.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_551.svg -> ../html-full/inherit_graph_1031.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_12.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_42.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_12.svg -> ../html-full/inherit_graph_42.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_501.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_921.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_501.svg -> ../html-full/inherit_graph_921.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_530.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_974.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_530.svg -> ../html-full/inherit_graph_974.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_606.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1154.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_606.svg -> ../html-full/inherit_graph_1154.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_280.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_501.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_280.svg -> ../html-full/inherit_graph_501.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_402.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_678.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_402.svg -> ../html-full/inherit_graph_678.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_598.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1128.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_598.svg -> ../html-full/inherit_graph_1128.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_245.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_440.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_245.svg -> ../html-full/inherit_graph_440.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_393.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_660.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_393.svg -> ../html-full/inherit_graph_660.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_449.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_763.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_449.svg -> ../html-full/inherit_graph_763.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_545.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1018.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_545.svg -> ../html-full/inherit_graph_1018.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_562.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1048.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_562.svg -> ../html-full/inherit_graph_1048.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_432.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_746.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_432.svg -> ../html-full/inherit_graph_746.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_426.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_740.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_426.svg -> ../html-full/inherit_graph_740.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_550.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1030.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_550.svg -> ../html-full/inherit_graph_1030.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_307.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_534.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_307.svg -> ../html-full/inherit_graph_534.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_567.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1059.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_567.svg -> ../html-full/inherit_graph_1059.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_534.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_985.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_534.svg -> ../html-full/inherit_graph_985.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_2.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_23.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_2.svg -> ../html-full/inherit_graph_23.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_582.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1097.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_582.svg -> ../html-full/inherit_graph_1097.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_591.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1113.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_591.svg -> ../html-full/inherit_graph_1113.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_13.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_44.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_13.svg -> ../html-full/inherit_graph_44.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_605.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1153.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_605.svg -> ../html-full/inherit_graph_1153.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_554.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1034.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_554.svg -> ../html-full/inherit_graph_1034.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_601.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1135.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_601.svg -> ../html-full/inherit_graph_1135.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_587.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1108.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_587.svg -> ../html-full/inherit_graph_1108.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_570.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1075.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_570.svg -> ../html-full/inherit_graph_1075.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_312.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_541.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_312.svg -> ../html-full/inherit_graph_541.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_76.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_176.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_76.svg -> ../html-full/inherit_graph_176.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_78.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_178.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_78.svg -> ../html-full/inherit_graph_178.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_423.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_737.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_423.svg -> ../html-full/inherit_graph_737.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_597.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1127.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_597.svg -> ../html-full/inherit_graph_1127.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_70.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_165.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_70.svg -> ../html-full/inherit_graph_165.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_524.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_964.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_524.svg -> ../html-full/inherit_graph_964.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_589.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1111.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_589.svg -> ../html-full/inherit_graph_1111.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_67.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_158.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_67.svg -> ../html-full/inherit_graph_158.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_538.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_996.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_538.svg -> ../html-full/inherit_graph_996.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_595.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1124.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_595.svg -> ../html-full/inherit_graph_1124.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_64.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_155.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_64.svg -> ../html-full/inherit_graph_155.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_77.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_177.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_77.svg -> ../html-full/inherit_graph_177.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_15.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_48.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_15.svg -> ../html-full/inherit_graph_48.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_301.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_526.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_301.svg -> ../html-full/inherit_graph_526.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_596.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1125.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_596.svg -> ../html-full/inherit_graph_1125.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_62.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_152.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_62.svg -> ../html-full/inherit_graph_152.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_3.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_24.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_3.svg -> ../html-full/inherit_graph_24.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_65.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_156.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_65.svg -> ../html-full/inherit_graph_156.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_425.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_739.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_425.svg -> ../html-full/inherit_graph_739.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_559.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1041.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_559.svg -> ../html-full/inherit_graph_1041.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_243.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_438.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_243.svg -> ../html-full/inherit_graph_438.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_16.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_49.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_16.svg -> ../html-full/inherit_graph_49.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_600.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1133.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_600.svg -> ../html-full/inherit_graph_1133.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_602.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_1138.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_602.svg -> ../html-full/inherit_graph_1138.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_406.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_690.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_406.svg -> ../html-full/inherit_graph_690.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_533.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_984.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_533.svg -> ../html-full/inherit_graph_984.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_23_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_23_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_23_dark.png -> ../html-full/form_23_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32_dark.png -> ../html-full/form_34_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_20.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20.png -> ../html-full/form_20.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32.png -> ../html-full/form_34.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sync_off.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sync_off.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sync_off.png -> ../html-full/sync_off.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sync_on.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/sync_on.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/sync_on.png -> ../html-full/sync_on.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_23.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_23.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_23.png -> ../html-full/form_23.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_25_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_25_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_25_dark.png -> ../html-full/form_25_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_25.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_25.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_25.png -> ../html-full/form_25.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plusd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plusd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plusd.svg -> ../html-full/plusd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plus.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/plus.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/plus.svg -> ../html-full/plus.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_8_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_8_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_8_dark.png -> ../html-full/form_8_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bc_s.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bc_s.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bc_s.png -> ../html-full/bc_s.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_8.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_8.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_8.png -> ../html-full/form_8.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bc_sd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/bc_sd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/bc_sd.png -> ../html-full/bc_sd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_21_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_21_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_21_dark.png -> ../html-full/form_21_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/minusd.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/minusd.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/minusd.svg -> ../html-full/minusd.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/minus.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/minus.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/minus.svg -> ../html-full/minus.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_19_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_19_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_19_dark.png -> ../html-full/form_19_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_9_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_9_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_9_dark.png -> ../html-full/form_9_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_21.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_21.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_21.png -> ../html-full/form_21.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_19.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_19.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_19.png -> ../html-full/form_19.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_28_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_30_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_28_dark.png -> ../html-full/form_30_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_9.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_9.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_9.png -> ../html-full/form_9.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_7_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_7_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_7_dark.png -> ../html-full/form_7_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_28.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_30.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_28.png -> ../html-full/form_30.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_17_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_17_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_17_dark.png -> ../html-full/form_17_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_44_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_58_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_44_dark.png -> ../html-full/form_58_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_7.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_7.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_7.png -> ../html-full/form_7.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_17.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_17.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_17.png -> ../html-full/form_17.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_30_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_32_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_30_dark.png -> ../html-full/form_32_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_44.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_58.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_44.png -> ../html-full/form_58.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_24_dark.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_24_dark.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_24_dark.png -> ../html-full/form_24_dark.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_30.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_32.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_30.png -> ../html-full/form_32.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_24.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_24.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_24.png -> ../html-full/form_24.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/splitbar.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/splitbar.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/splitbar.png -> ../html-full/splitbar.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/splitbard.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/splitbard.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/splitbard.png -> ../html-full/splitbard.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_sd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_sd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_sd.png -> ../html-full/tab_sd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_s.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_s.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_s.png -> ../html-full/tab_s.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_hd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_hd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_hd.png -> ../html-full/tab_hd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_h.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_h.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_h.png -> ../html-full/tab_h.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_bd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_bd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_bd.png -> ../html-full/tab_bd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_fd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_fd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_fd.png -> ../html-full/nav_fd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_b.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_b.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_b.png -> ../html-full/tab_b.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_f.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_f.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_f.png -> ../html-full/nav_f.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_a.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_a.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_a.png -> ../html-full/tab_a.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_ad.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_ad.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_ad.png -> ../html-full/tab_ad.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/closed.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/closed.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/closed.png -> ../html-full/closed.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/open.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/open.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/open.png -> ../html-full/open.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_hd.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_hd.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_hd.png -> ../html-full/nav_hd.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_h.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_h.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_h.png -> ../html-full/nav_h.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_g.png -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/nav_g.png changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/nav_g.png -> ../html-full/nav_g.png absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> ../../html-full/search/search.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1d.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> all_1d.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> ../../html-full/search/search.css absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enumvalues_13.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> ../../html-full/search/enumvalues_13.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_5.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> ../../html-full/search/groups_5.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_b.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_b.js -> ../../html-full/search/groups_b.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_0.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_0.js -> ../../html-full/search/groups_0.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_e.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_e.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_e.js -> ../../html-full/search/groups_e.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_f.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_f.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_f.js -> ../../html-full/search/groups_f.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_8.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_6.js -> ../../html-full/search/related_8.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_7.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_7.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_7.js -> ../../html-full/search/groups_7.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> ../../html-full/search/groups_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_14.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_14.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_14.js -> ../../html-full/search/enums_14.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_0.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> ../../html-full/search/pages_0.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_2.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_2.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_2.js -> ../../html-full/search/groups_2.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> ../../html-full/search/groups_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_4.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_4.js -> ../../html-full/search/groups_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_f.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_10.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_f.js -> ../../html-full/search/pages_10.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_sel.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> ../../html-full/search/mag_sel.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_seld.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_seld.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_seld.svg -> ../../html-full/search/mag_seld.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_6.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> ../../html-full/search/groups_6.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> ../../html-full/search/pages_5.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/close.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/close.svg -> ../../html-full/search/close.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_a.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.js -> ../../html-full/search/enums_a.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_8.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> ../../html-full/search/groups_8.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag.svg -> ../../html-full/search/mag.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_d.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> ../../html-full/search/mag_d.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_d.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_f.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_d.js -> ../../html-full/search/related_f.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_1.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_0.js -> ../../html-full/search/related_1.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> ../../html-full/search/groups_3.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_10.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> ../../html-full/search/groups_10.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_3.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_3.js -> ../../html-full/search/pages_3.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> ../../html-full/search/related_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_d.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> ../../html-full/search/groups_d.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_b.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> ../../html-full/search/pages_b.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_12.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> ../../html-full/search/pages_12.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_19.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_19.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_19.js -> ../../html-full/search/functions_19.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_3.js -> ../../html-full/search/related_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1a.js -> all_1c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_a.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> ../../html-full/search/groups_a.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_1.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> ../../html-full/search/groups_1.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_e.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_b.js -> ../../html-full/search/defines_e.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_7.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> ../../html-full/search/pages_7.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> ../../html-full/search/pages_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_4.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_5.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_4.js -> ../../html-full/search/related_5.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_11.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_11.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_11.js -> ../../html-full/search/groups_11.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_6.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_6.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_6.js -> ../../html-full/search/pages_6.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_10.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_11.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_10.js -> ../../html-full/search/pages_11.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_1.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> ../../html-full/search/pages_1.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> ../../html-full/search/enums_13.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_9.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_9.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_9.js -> ../../html-full/search/pages_9.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> ../../html-full/search/related_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_7.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> ../../html-full/search/related_7.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_c.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_c.js -> ../../html-full/search/pages_c.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> ../../html-full/search/defines_0.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_d.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_e.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_d.js -> ../../html-full/search/pages_e.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_8.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_a.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_8.js -> ../../html-full/search/defines_a.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_f.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_f.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_f.js -> ../../html-full/search/enums_f.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_15.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> ../../html-full/search/enums_15.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StatePropagatorData_1_1Element__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StatePropagatorData_1_1Element__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StatePropagatorData_1_1Element__inherit__graph.svg -> classgmx_1_1StatePropagatorData_1_1Element__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ForceElement__inherit__graph.svg -> classgmx_1_1ForceElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__inherit__graph.svg -> classgmx_1_1internal_1_1BasicAverageHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyData_1_1Element__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyData_1_1Element__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergyData_1_1Element__inherit__graph.svg -> classgmx_1_1EnergyData_1_1Element__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConstraintsElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConstraintsElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ConstraintsElement__inherit__graph.svg -> classgmx_1_1ConstraintsElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.svg -> classgmx_1_1AnalysisDataLifetimeModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataAverageModule__inherit__graph.svg -> classgmx_1_1AnalysisDataAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02electricfield_8cpp_03_1_1ElectricField__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02electricfield_8cpp_03_1_1ElectricField__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02electricfield_8cpp_03_1_1ElectricField__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02electricfield_8cpp_03_1_1ElectricField__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataBinAverageModule__inherit__graph.svg -> classgmx_1_1AnalysisDataBinAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02scattering_8cpp_03_1_1ScatteringModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02scattering_8cpp_03_1_1ScatteringModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02scattering_8cpp_03_1_1ScatteringModule__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02scattering_8cpp_03_1_1ScatteringModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02dssp_8cpp_03_1_1DsspModuleTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02dssp_8cpp_03_1_1DsspModuleTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02dssp_8cpp_03_1_1DsspModuleTest__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02dssp_8cpp_03_1_1DsspModuleTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1GyrateModuleTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1GyrateModuleTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1GyrateModuleTest__inherit__graph.svg -> classgmx_1_1test_1_1GyrateModuleTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1HbondModuleTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1HbondModuleTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1HbondModuleTest__inherit__graph.svg -> classgmx_1_1test_1_1HbondModuleTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02histogram_8cpp_03_1_1MockAverageHistogram__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02histogram_8cpp_03_1_1MockAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02histogram_8cpp_03_1_1MockAverageHistogram__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02histogram_8cpp_03_1_1MockAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02histogram_8cpp_03_1_1StaticAverageHistogram__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02histogram_8cpp_03_1_1StaticAverageHistogram__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02histogram_8cpp_03_1_1StaticAverageHistogram__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02histogram_8cpp_03_1_1StaticAverageHistogram__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__inherit__graph.svg -> classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ComputeGlobalsElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ComputeGlobalsElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ComputeGlobalsElement__inherit__graph.svg -> classgmx_1_1ComputeGlobalsElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.svg -> classgmx_1_1AnalysisDataWeightedHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.svg -> classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSectionHandle__inherit__graph.svg -> classgmx_1_1OptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VelocityScalingTemperatureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VelocityScalingTemperatureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VelocityScalingTemperatureCoupling__inherit__graph.svg -> classgmx_1_1VelocityScalingTemperatureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectoryElement__inherit__graph.svg -> classgmx_1_1TrajectoryElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule__inherit__graph.svg -> classgmx_1_1AnalysisDataFrameAverageModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FreeEnergyPerturbationData_1_1Element__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FreeEnergyPerturbationData_1_1Element__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FreeEnergyPerturbationData_1_1Element__inherit__graph.svg -> classgmx_1_1FreeEnergyPerturbationData_1_1Element__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.svg -> classgmx_1_1AnalysisDataDisplacementModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionStorage__inherit__graph.svg -> classgmx_1_1DoubleOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionStorage__inherit__graph.svg -> classgmx_1_1FloatOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionStorage__inherit__graph.svg -> classgmx_1_1StringOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionStorage__inherit__graph.svg -> classgmx_1_1BooleanOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionStorage__inherit__graph.svg -> classgmx_1_1FileNameOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataVectorPlotModule__inherit__graph.svg -> classgmx_1_1AnalysisDataVectorPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__inherit__graph.svg -> classgmx_1_1IntegerOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionStorage__inherit__graph.svg -> classgmx_1_1EnumOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__inherit__graph.svg -> classgmx_1_1Int64OptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergySignaller__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergySignaller__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnergySignaller__inherit__graph.svg -> classgmx_1_1EnergySignaller__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParrinelloRahmanBarostat__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParrinelloRahmanBarostat__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParrinelloRahmanBarostat__inherit__graph.svg -> classgmx_1_1ParrinelloRahmanBarostat__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExpandedEnsembleElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExpandedEnsembleElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExpandedEnsembleElement__inherit__graph.svg -> classgmx_1_1ExpandedEnsembleElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataPlotModule__inherit__graph.svg -> classgmx_1_1AnalysisDataPlotModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02timeunitmanager_8cpp_03_1_1TimeOptionScaler__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02timeunitmanager_8cpp_03_1_1TimeOptionScaler__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02timeunitmanager_8cpp_03_1_1TimeOptionScaler__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02timeunitmanager_8cpp_03_1_1TimeOptionScaler__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02extract__cluster_8cpp_03_1_1ExtractClusterModuleTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02extract__cluster_8cpp_03_1_1ExtractClusterModuleTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02extract__cluster_8cpp_03_1_1ExtractClusterModuleTest__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02extract__cluster_8cpp_03_1_1ExtractClusterModuleTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOptionStorage__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02select_8cpp_03_1_1IndexFileWriterModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02select_8cpp_03_1_1IndexFileWriterModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02select_8cpp_03_1_1IndexFileWriterModule__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02select_8cpp_03_1_1IndexFileWriterModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1RootHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1RootHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1RootHelpTopic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1RootHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__inherit__graph.svg -> classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LegacyEnumOption__inherit__graph.svg -> classgmx_1_1LegacyEnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__inherit__graph.svg -> classgmx_1_1EnumOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionStorageTemplateSimple__inherit__graph.svg -> classgmx_1_1OptionStorageTemplateSimple__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeHelpTopic__inherit__graph.svg -> classgmx_1_1CompositeHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError__inherit__graph.svg -> classgmx_1_1SimulationAlgorithmSetupError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimpleHelpTopic__inherit__graph.svg -> classgmx_1_1SimpleHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError__inherit__graph.svg -> classgmx_1_1ParallelConsistencyError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionStorage__inherit__graph.svg -> classgmx_1_1SelectionOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LastStepSignaller__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LastStepSignaller__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LastStepSignaller__inherit__graph.svg -> classgmx_1_1LastStepSignaller__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FirstOrderPressureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FirstOrderPressureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FirstOrderPressureCoupling__inherit__graph.svg -> classgmx_1_1FirstOrderPressureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOption__inherit__graph.svg -> classgmx_1_1FloatOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOption__inherit__graph.svg -> classgmx_1_1FileNameOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64Option__inherit__graph.svg -> classgmx_1_1Int64Option__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataProxy__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataProxy__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataProxy__inherit__graph.svg -> classgmx_1_1AnalysisDataProxy__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__inherit__graph.svg -> classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOption__inherit__graph.svg -> classgmx_1_1DoubleOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOption__inherit__graph.svg -> classgmx_1_1StringOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOption__inherit__graph.svg -> classgmx_1_1SelectionOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Options__inherit__graph.svg -> classgmx_1_1Options__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOption__inherit__graph.svg -> classgmx_1_1BooleanOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointHelper__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointHelper__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointHelper__inherit__graph.svg -> classgmx_1_1CheckpointHelper__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PullElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PullElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PullElement__inherit__graph.svg -> classgmx_1_1PullElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisArrayData__inherit__graph.svg -> classgmx_1_1AnalysisArrayData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError__inherit__graph.svg -> classgmx_1_1ElementNotFoundError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__inherit__graph.svg -> classgmx_1_1InconsistentInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectorySignaller__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectorySignaller__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TrajectorySignaller__inherit__graph.svg -> classgmx_1_1TrajectorySignaller__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError__inherit__graph.svg -> classgmx_1_1CheckpointError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__inherit__graph.svg -> classgmx_1_1InvalidInputError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggingSignaller__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggingSignaller__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1LoggingSignaller__inherit__graph.svg -> classgmx_1_1LoggingSignaller__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError__inherit__graph.svg -> classgmx_1_1NotImplementedError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesplinespreadtest_8cpp_03_1_1SplineAndSpreadTestBody__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesplinespreadtest_8cpp_03_1_1SplineAndSpreadTestBody__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesplinespreadtest_8cpp_03_1_1SplineAndSpreadTestBody__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02pmesplinespreadtest_8cpp_03_1_1SplineAndSpreadTestBody__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1SynopsisFormatter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1SynopsisFormatter__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1SynopsisFormatter__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1SynopsisFormatter__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToString__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToString__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToString__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToString__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesolvetest_8cpp_03_1_1SolveTestBody__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesolvetest_8cpp_03_1_1SolveTestBody__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmesolvetest_8cpp_03_1_1SolveTestBody__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02pmesolvetest_8cpp_03_1_1SolveTestBody__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmegathertest_8cpp_03_1_1GatherTestBody__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmegathertest_8cpp_03_1_1GatherTestBody__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02pmegathertest_8cpp_03_1_1GatherTestBody__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02pmegathertest_8cpp_03_1_1GatherTestBody__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterFileNoThrow__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterFileNoThrow__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterFileNoThrow__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterFileNoThrow__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterTextWriter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterTextWriter__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterTextWriter__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterTextWriter__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistanceModuleData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistanceModuleData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistanceModuleData__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistanceModuleData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterString__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterString__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterString__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02exceptions_8cpp_03_1_1MessageWriterString__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02analysismodule_8cpp_03_1_1TrajectoryAnalysisModuleDataBasic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02analysismodule_8cpp_03_1_1TrajectoryAnalysisModuleDataBasic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02analysismodule_8cpp_03_1_1TrajectoryAnalysisModuleDataBasic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02analysismodule_8cpp_03_1_1TrajectoryAnalysisModuleDataBasic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1RdfModuleData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1RdfModuleData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1RdfModuleData__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1RdfModuleData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinemodulemanager_8cpp_03_1_1CMainCommandLineModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinemodulemanager_8cpp_03_1_1CMainCommandLineModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinemodulemanager_8cpp_03_1_1CMainCommandLineModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinemodulemanager_8cpp_03_1_1CMainCommandLineModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultOutputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultOutputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultOutputRedirector__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultOutputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultInputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultInputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultInputRedirector__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02fileredirector_8cpp_03_1_1DefaultInputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02freevolume_8cpp_03_1_1FreeVolume__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02freevolume_8cpp_03_1_1FreeVolume__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02freevolume_8cpp_03_1_1FreeVolume__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02freevolume_8cpp_03_1_1FreeVolume__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistance__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistance__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistance__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02pairdist_8cpp_03_1_1PairDistance__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02programcontext_8cpp_03_1_1DefaultProgramContext__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02programcontext_8cpp_03_1_1DefaultProgramContext__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02programcontext_8cpp_03_1_1DefaultProgramContext__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02programcontext_8cpp_03_1_1DefaultProgramContext__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02msd_8cpp_03_1_1MsdMatcher__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02msd_8cpp_03_1_1MsdMatcher__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02msd_8cpp_03_1_1MsdMatcher__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02msd_8cpp_03_1_1MsdMatcher__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__inherit__graph.svg -> classgmx_1_1ThreeFry2x64__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__inherit__graph.svg -> classgmx_1_1ThreeFry2x64Fast__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__inherit__graph.svg -> classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02testinit_8cpp_03_1_1TestProgramContext__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02testinit_8cpp_03_1_1TestProgramContext__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1anonymous__namespace_02testinit_8cpp_03_1_1TestProgramContext__inherit__graph.svg -> classgmx_1_1test_1_1anonymous__namespace_02testinit_8cpp_03_1_1TestProgramContext__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTestNoMemCopyable__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTestNoMemCopyable__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTestNoMemCopyable__inherit__graph.svg -> structgmx_1_1test_1_1HostAllocatorTestNoMemCopyable__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.svg -> classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule__stub_8cpp_03_1_1ColvarsMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule__stub_8cpp_03_1_1ColvarsMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule__stub_8cpp_03_1_1ColvarsMDModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02colvarsMDModule__stub_8cpp_03_1_1ColvarsMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule__stub_8cpp_03_1_1PlumedMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule__stub_8cpp_03_1_1PlumedMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule__stub_8cpp_03_1_1PlumedMDModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02plumedMDModule__stub_8cpp_03_1_1PlumedMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule_8cpp_03_1_1ColvarsMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule_8cpp_03_1_1ColvarsMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02colvarsMDModule_8cpp_03_1_1ColvarsMDModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02colvarsMDModule_8cpp_03_1_1ColvarsMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsModifyingTypeVisitor__inherit__graph.svg -> classgmx_1_1OptionsModifyingTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMOutputProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMOutputProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMOutputProvider__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMOutputProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__inherit__graph.svg -> structgmx_1_1OpenClTraits_3_01cl__command__queue_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__inherit__graph.svg -> classgmx_1_1RepeatingOptionSectionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.svg -> structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.svg -> structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.svg -> structgmx_1_1test_1_1HostAllocatorTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__inherit__graph.svg -> structgmx_1_1OpenClTraits_3_01cl__kernel_01_4__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage__inherit__graph.svg -> classgmx_1_1SelectionFileOptionStorage__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__inherit__graph.svg -> classgmx_1_1OptionsTypeVisitor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.svg -> classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.svg -> classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.svg -> classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.svg -> classgmx_1_1test_1_1MockOptionsModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule_8cpp_03_1_1PlumedMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule_8cpp_03_1_1PlumedMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02plumedMDModule_8cpp_03_1_1PlumedMDModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02plumedMDModule_8cpp_03_1_1PlumedMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02densityfitting_8cpp_03_1_1DensityFitting__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02densityfitting_8cpp_03_1_1DensityFitting__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02densityfitting_8cpp_03_1_1DensityFitting__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02densityfitting_8cpp_03_1_1DensityFitting__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverTemperatureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverTemperatureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverTemperatureCoupling__inherit__graph.svg -> classgmx_1_1NoseHooverTemperatureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PmeLoadBalanceHelper__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PmeLoadBalanceHelper__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PmeLoadBalanceHelper__inherit__graph.svg -> classgmx_1_1PmeLoadBalanceHelper__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOutputProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOutputProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOutputProvider__inherit__graph.svg -> classgmx_1_1DensityFittingOutputProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VRescaleTemperatureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VRescaleTemperatureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1VRescaleTemperatureCoupling__inherit__graph.svg -> classgmx_1_1VRescaleTemperatureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionTemplate__inherit__graph.svg -> classgmx_1_1OptionTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ExactTextMatch__inherit__graph.svg -> classgmx_1_1test_1_1ExactTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Propagator__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Propagator__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Propagator__inherit__graph.svg -> classgmx_1_1Propagator__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AndersenTemperatureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AndersenTemperatureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AndersenTemperatureCoupling__inherit__graph.svg -> classgmx_1_1AndersenTemperatureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomDecHelper__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomDecHelper__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DomDecHelper__inherit__graph.svg -> classgmx_1_1DomDecHelper__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotTopologyPreprocessor__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotTopologyPreprocessor__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotTopologyPreprocessor__inherit__graph.svg -> classgmx_1_1NNPotTopologyPreprocessor__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BerendsenTemperatureCoupling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BerendsenTemperatureCoupling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BerendsenTemperatureCoupling__inherit__graph.svg -> classgmx_1_1BerendsenTemperatureCoupling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingForceProvider__inherit__graph.svg -> classgmx_1_1DensityFittingForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoTextMatch__inherit__graph.svg -> classgmx_1_1test_1_1NoTextMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__inherit__graph.svg -> classgmx_1_1ExceptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02nnpot_8cpp_03_1_1NNPotMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02nnpot_8cpp_03_1_1NNPotMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02nnpot_8cpp_03_1_1NNPotMDModule__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02nnpot_8cpp_03_1_1NNPotMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__inherit__graph.svg -> classgmx_1_1SimulationInstabilityError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__inherit__graph.svg -> classgmx_1_1test_1_1ConfMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1XvgMatch__inherit__graph.svg -> classgmx_1_1test_1_1XvgMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InteractiveMolecularDynamics__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InteractiveMolecularDynamics__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InteractiveMolecularDynamics__inherit__graph.svg -> classgmx_1_1InteractiveMolecularDynamics__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetStartTimeTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetStartTimeTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetStartTimeTest__inherit__graph.svg -> classgmx_1_1test_1_1SetStartTimeTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMM__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMM__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMM__inherit__graph.svg -> classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMM__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.svg -> structgmx_1_1Constraints_1_1CreationHelper__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetBothTimeTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetBothTimeTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetBothTimeTest__inherit__graph.svg -> classgmx_1_1test_1_1SetBothTimeTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetTimeStepTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetTimeStepTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetTimeStepTest__inherit__graph.svg -> classgmx_1_1test_1_1SetTimeStepTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.svg -> classgmx_1_1RepeatingOptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsTest__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1SetAtomsTest__inherit__graph.svg -> classgmx_1_1test_1_1SetAtomsTest__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclBbfft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclBbfft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclBbfft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplSyclBbfft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclRocfft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclRocfft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclRocfft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplSyclRocfft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__inherit__graph.svg -> classgmx_1_1CommandLineProgramContext__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionValueStoreNull__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionValueStoreNull__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionValueStoreNull__inherit__graph.svg -> classgmx_1_1OptionValueStoreNull__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ProcessFrameConversion__inherit__graph.svg -> classgmx_1_1ProcessFrameConversion__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OutputSelector__inherit__graph.svg -> classgmx_1_1OutputSelector__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__inherit__graph.svg -> classgmx_1_1SelectionFileOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipRocfft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipRocfft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipRocfft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplHipRocfft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__inherit__graph.svg -> classgmx_1_1CommandLineHelpModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsData__inherit__graph.svg -> classgmx_1_1NoseHooverChainsData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSycl__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSycl__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSycl__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplSycl__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetVelocities__inherit__graph.svg -> classgmx_1_1SetVelocities__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclVkfft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclVkfft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclVkfft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplSyclVkfft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOXdrSerializer__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOXdrSerializer__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOXdrSerializer__inherit__graph.svg -> classgmx_1_1FileIOXdrSerializer__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipVkFft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipVkFft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplHipVkFft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplHipVkFft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOclVkfft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOclVkfft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOclVkfft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplOclVkfft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionInfo__inherit__graph.svg -> classgmx_1_1SelectionOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOption__inherit__graph.svg -> classgmx_1_1SelectionFileOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NoseHooverChainsElement__inherit__graph.svg -> classgmx_1_1NoseHooverChainsElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionManager__inherit__graph.svg -> classgmx_1_1SelectionOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> classgmx_1_1test_1_1TextFileMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FloatOptionInfo__inherit__graph.svg -> classgmx_1_1FloatOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__inherit__graph.svg -> classgmx_1_1Int64OptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetTimeStep__inherit__graph.svg -> classgmx_1_1SetTimeStep__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetPrecision__inherit__graph.svg -> classgmx_1_1SetPrecision__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__inherit__graph.svg -> classgmx_1_1BooleanOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockModule__inherit__graph.svg -> classgmx_1_1test_1_1MockModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFft__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFft__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFft__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplCuFft__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkData__inherit__graph.svg -> classgmx_1_1MttkData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1NoContentsMatch__inherit__graph.svg -> classgmx_1_1test_1_1NoContentsMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetStartTime__inherit__graph.svg -> classgmx_1_1SetStartTime__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__inherit__graph.svg -> classgmx_1_1SelectionOptionBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__inherit__graph.svg -> classgmx_1_1StringOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetForces__inherit__graph.svg -> classgmx_1_1SetForces__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeSimulatorElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeSimulatorElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CompositeSimulatorElement__inherit__graph.svg -> classgmx_1_1CompositeSimulatorElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__inherit__graph.svg -> classgmx_1_1DoubleOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclMkl__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclMkl__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplSyclMkl__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplSyclMkl__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOcl__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOcl__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplOcl__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplOcl__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__inherit__graph.svg -> classgmx_1_1StringOutputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkBoxScaling__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkBoxScaling__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkBoxScaling__inherit__graph.svg -> classgmx_1_1MttkBoxScaling__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionInfo__inherit__graph.svg -> classgmx_1_1FileNameOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__inherit__graph.svg -> classgmx_1_1FileNameOptionManager__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFftMp__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFftMp__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Gpu3dFft_1_1ImplCuFftMp__inherit__graph.svg -> classgmx_1_1Gpu3dFft_1_1ImplCuFftMp__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOptionInfo__inherit__graph.svg -> classgmx_1_1EnumOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintForceProvider__inherit__graph.svg -> classgmx_1_1RestraintForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ToleranceError__inherit__graph.svg -> classgmx_1_1ToleranceError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOptions__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOptions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DensityFittingOptions__inherit__graph.svg -> classgmx_1_1DensityFittingOptions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__inherit__graph.svg -> classgmx_1_1IntegerOptionInfo__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TimeUnitBehavior__inherit__graph.svg -> classgmx_1_1TimeUnitBehavior__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetAtoms__inherit__graph.svg -> classgmx_1_1SetAtoms__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classAnalysisTemplate__inherit__graph.svg -> classAnalysisTemplate__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkElement__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkElement__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MttkElement__inherit__graph.svg -> classgmx_1_1MttkElement__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SetBox__inherit__graph.svg -> classgmx_1_1SetBox__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1Msd__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1Msd__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1Msd__inherit__graph.svg -> classgmx_1_1analysismodules_1_1Msd__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestException__inherit__graph.svg -> classgmx_1_1test_1_1TestException__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionSection__inherit__graph.svg -> classgmx_1_1OptionSection__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SansDebye__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SansDebye__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SansDebye__inherit__graph.svg -> classgmx_1_1SansDebye__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ColvarsOptions__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ColvarsOptions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ColvarsOptions__inherit__graph.svg -> classgmx_1_1ColvarsOptions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PlumedForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PlumedForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PlumedForceProvider__inherit__graph.svg -> classgmx_1_1PlumedForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.svg -> classgmx_1_1StandardInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SaxsDebye__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SaxsDebye__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SaxsDebye__inherit__graph.svg -> classgmx_1_1SaxsDebye__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__inherit__graph.svg -> classgmx_1_1RangeError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.svg -> classgmx_1_1AnalysisData__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NeighborSearchSignaller__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NeighborSearchSignaller__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NeighborSearchSignaller__inherit__graph.svg -> classgmx_1_1NeighborSearchSignaller__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InternalError__inherit__graph.svg -> classgmx_1_1InternalError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMForceProvider__inherit__graph.svg -> classgmx_1_1QMMMForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyHolder__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyHolder__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TopologyHolder__inherit__graph.svg -> classgmx_1_1TopologyHolder__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.svg -> classgmx_1_1StringInputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.svg -> classgmx_1_1FileIOError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TorchModel__inherit__graph.svg -> classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> classgmx_1_1RestraintMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> classgmx_1_1SwapCoordinates__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__inherit__graph.svg -> classgmx_1_1QMMMOptions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> classgmx_1_1TextInputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__inherit__graph.svg -> classgmx_1_1NNPotForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> classgmx_1_1TextOutputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__inherit__graph.svg -> classgmx_1_1ModularSimulator__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_1e.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> all_1e.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_2.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> all_2.js dh_bash-completion -i dh_lintian -i dh_link -i dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2025.0-2_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs10 -L libgromacs10 -l debian/libgromacs10/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -plibnblib-gmx0 -L libnblib-gmx0 -l debian/libnblib-gmx0/usr/lib:debian/libgromacs10/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -pgromacs -L libgromacs10 -l debian/libgromacs10/usr/lib:debian/gromacs/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libnblib-gmx-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs' in '../gromacs_2025.0-2_arm64.deb'. dpkg-deb: building package 'libgromacs10' in '../libgromacs10_2025.0-2_arm64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2025.0-2_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2025.0-2_arm64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2025.0-2_arm64.deb'. dpkg-deb: building package 'libnblib-gmx-dev' in '../libnblib-gmx-dev_2025.0-2_arm64.deb'. dpkg-deb: building package 'libgromacs10-dbgsym' in '../libgromacs10-dbgsym_2025.0-2_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2025.0-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gromacs_2025.0-2_arm64.buildinfo dpkg-genchanges --build=binary -O../gromacs_2025.0-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2526377 and its subdirectories I: Current time: Mon Feb 17 02:32:32 -12 2025 I: pbuilder-time-stamp: 1739802752